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PDB ID Mentions in PubMed Central Article count: 10

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PDB ID Mentions in PubMed Central

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Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19465773 | PubMedCentral: PMC2685735 | DOI: 10.1107/S0907444909012098

The structures from the PHENIX library included 1029B (PDB code 1n0e; Chen et al. , 2004 ▶ ), 1038B (1lql; Choi et al. , 2003 ▶ ), 1063B (1lfp; Shin et al. , 2002 ▶ ), 1071B (1... f2; Shin, Roberts et al. , 2003 ▶ ), 1102B (1l2f; Shin, Nguyen et al. , 2003 ▶ ), 1167B (1s12; Shin et al. , 2005 ▶ ), aep-transaminase (1m32; Chen et al. , 2002 ▶ ), armadillo (3bct; Huber et al. , 1997 ▶ ), calmodulin (1exr; Wilson & Brunger, 2000 ▶ ), cobd (1kus; Cheong et al. , 2002 ▶ ), cp-synthase (1l1e; Huang et al. , 2002 ▶ ), cyanase (1dw9; Walsh et al. , 2000 ▶ ), epsin (1edu; Hyman et al. , 2000 ▶ ), flr (1bkj; Tanner et al. , 1996 ▶ ), fusion-complex (1sfc; Sutton et al. , 1998 ▶ ), gene-5 (1vqb; Skinner et al. , 1994 ▶ ), gere (1fse; Ducros et al. , 2001 ▶ ), gpatase (1ecf; Muchmore et al. , 1998 ▶ ), granulocyte (2gmf; Rozwarski et al. , 1996 ▶ ), groEL (1oel; Braig et al. , 1995 ▶ ), group2-intron (1kxk; Zhang & Doudna, 2002 ▶ ), hn-rnp (1ha1; Shamoo et al. , 1997 ▶ ), ic-lyase (1f61; Sharma et al. , 2000 ▶ ), insulin (2bn3; Nanao et al. , 2005 ▶ ), lysozyme (unpublished results; CSHL Macromolecular Crystallo­graphy Course), mbp (1ytt; Burling et al. , 1996 ▶ ), mev-kinase (1kkh; Yang et al. , 2002 ▶ ), myoglobin (A. Gonzales, personal communication), nsf-d2 (1nsf; Yu et al. , 1998 ▶ ), nsf-n (1qcs; Yu et al. , 1999 ▶ ), p32 (1p32; Jiang et al. , 1999 ▶ ), p9 (1bkb; Peat et al. , 1998 ▶ ), pdz (1kwa; Daniels et al. , 1998 ▶ ), penicillopepsin (3app; James & Sielecki, 1983 ▶ ), psd-95 (1jxm; Tavares et al. , 2001 ▶ ), qaprtase (1qpo; Sharma et al. , 1998 ▶ ), rab3a (1zbd; Ostermeier & Brunger, 1999 ▶ ), rh-dehalogenase (1bn7; Newman et al. , 1999 ▶ ), rnase-p (1nz0; Kazantsev et al. , 2003 ▶ ), rnase-s (1rge; Sevcik et al. , 1996 ▶ ), rop (1f4n; Willis et al. , 2000 ▶ ), s-hydrolase (1a7a; Turner et al. , 1998 ▶ ), sec17 (1qqe; Rice & Brunger, 1999 ▶ ), synapsin (1auv; Esser et al. , 1998 ▶ ), synaptotagmin (1dqv; Sutton et al. , 1999 ▶ ), tryparedoxin (1qk8; Alphey et al. , 1999 ▶ ), ut-synthase (1e8c; Gordon et al. , 2001 ▶ ) and vmp ( l8w; Eicken et al. , 2002 ▶ ).

( c ) Structures determined using MIR: flr (1bkj; Tanner et al. , 1996 ▶ ), granulocyte (2gmf; Rozwarski et al. , 1996 ▶ ), groEL (1oel; Braig et al. , 1995 ▶ ), hn-rnp (1ha1; Shamoo et al. , 1997 ▶ ), penicillopepsin (3app; James & Sielecki, 1983 ▶ ), qaprtase (1qpo; Sharma et al. , 1998 ▶ ), rh-dehalogenase (1bn7; Newman et al. , 1999 ▶ ), rnase-s (1rge; Sevcik et al. , 1996 ▶ ), rop (1f4n; Willis et al. , 2000 ▶ ) and synaptotagmin (1dqv; Sutton et al. , 1999 ▶ ).

Publication Year: 2009


Automatic multiple-zone rigid-body refinement with a large convergence radius.

(2009) J Appl Crystallogr 42

PubMed: 19649324 | PubMedCentral: PMC2712840 | DOI: 10.1107/S0021889809023528

NA PDB ID NB group2-intron 3.5 1497 1kxk 1 synaptotagmin 3.2 2186 1dqv   1029B 3.0 9230 1n0e   1038B 3.0 11038 1lql 5 1071B 3.0 6558 1nf2 6 proteasome 2.9 24927 1q5q   sec17 2.... 2217 1qqe   cp-synthase 2.8 4331 1l1e   penicillopepsin 2.8 2366 3app   s-hydrolase 2.8 6666 1a7a   ut-synthase 2.8 7504 1e8c   gere 2.7 3060 1fse   groel 2.7 26957 1oel   aep-transaminase 2.6 16698 1m32 4 rab3a 2.6 2431 1zbd   a2u-globulin 2.5 5148 2a2u 4 flavin-reductase 2.5 3385 1bkj   p32 2.5 4265 1p32   psd-95 2.5 2180 1jxm   qaprtase 2.5 12570 1qpo 1 rnase-s 2.5 1488 1rge   1102B 2.5 2662 1l2f   rh-dehalogenase 2.45 2336 1bn7   armadillo 2.4 3458 3bct   cyanase 2.4 11970 1dw9   fusion-complex 2.4 7025 1sfc   human-otc 2.4 2528 1ep9   mev-kinase 2.4 2506 1kkh   nsf-d2 2.4 1943 1nsf   granulocyte 2.35 1908 2gmf   oat-gabaculine 2.3 9450 1gbn 2 vmp 2.3 7992 1l8w   gpatase 2.25 7786 1ecf   hn-rnp 2.2 1338 1ha1   antitrypsin 2.1 2985 1hp7   pdz 2.1 1372 1kwa   1167B 2.0 2920 1s12   apoferritin 2.0 1354 1gwg   cobd 2.0 2738 1lkc   synapsin 2.0 4636 1auv 1 tryparedoxin 2.0 1145 1qk8   myoglobin 1.9 1227 1n9x   nsf-n 1.9 1518 1qcs   rop 1.9 850 1f4n   epsin 1.8 1210 1edu   gene-5 1.8 673 1vqb 2 ic lyase 1.8 6484 1f61   mbp 1.8 1760 1ytt   p9 1.75 1062 1bkb   1063B 1.7 1926 1lfp   nitrite-reduct 1.7 2582 1et7   insulin 1.7 400 2bn3   lysozyme 1.5 982 1aki   rnase-p 1.5 3607 1nz0   calmodulin 1.1 1150 1exr 2 hipip 0.8 616 1iua   Table 2 Comparison of success rates for different values of the n_ref(1) 1 parameter (§3.2.1 ) The first row and the first column show the parameter values.

Publication Year: 2009


Rapid model building of alpha-helices in electron-density maps.

(2010) Acta Crystallogr D Biol Crystallogr 66

PubMed: 20179338 | PubMedCentral: PMC2827347 | DOI: 10.1107/S0907444910000314

Table 1 Helix identification in experimental electron-density maps   Residues         Structure Total Helix Built Correct d min () Map quality (CC to model map)... R.m.s.d. () Helixmap CC RNase P ( 1nz0 ; Kazantsev et al. , 2003 ▶ ) 416 177 6 6 1.5 0.53 0.85 0.41 1063B ( 1lfp ; Shin et al. , 2002 ▶ ) 243 92 65 58 1.7 0.68 1.57 0.42 Epsin ( 1edu ; Hyman et al. , 2000 ▶ ) 149 100 98 83 1.8 0.89 0.97 0.62 Isocitrate lyase ( 1f61 ; Sharma et al. , 2000 ▶ ) 836 387 385 286 1.8 0.65 1.44 0.51 MBP ( 1ytt ; Burling et al. , 1996 ▶ ) 227 42 30 17 1.8 0.89 1.31 0.52 P9 ( 1bkb ; Peat et al. , 1998 ▶ ) 136 4 27 0 1.8 0.81 2.11 0.30 Penicillopepsin ( 3app ; James Sielecki, 1983 ▶ ) 323 30 33 0 1.8 0.84 2.06 0.28 Myoglobin (Ana Gonzlez, personal communication) 154 110 59 54 1.9 0.73 0.86 0.51 ROP ( 1f4n ; Willis et al. , 2000 ▶ ) 108 92 97 86 1.9 0.84 0.89 0.54 1167B ( 1s12 ; Shin et al. , 2005 ▶ ) 370 160 142 118 2.0 0.72 1.12 0.50 CobD ( 1kus ; Cheong et al. , 2002 ▶ ) 355 129 61 45 2.0 0.80 1.29 0.46 NSF-N ( 1qcs ; Yu et al. , 1999 ▶ ) 195 29 24 2 2.0 0.80 2.21 0.22 Synapsin ( 1auv ; Esser et al. , 1998 ▶ ) 585 149 74 45 2.0 0.78 1.58 0.42 Tryparedoxin ( 1qk8 ; Alphey et al. , 1999 ▶ ) 143 40 8 0 2.0 0.79 2.12 0.18 PDZ ( 1kwa ; Daniels et al. , 1998 ▶ ) 174 30 19 0 2.1 0.67 2.16 0.22 Fusion complex ( 1sfc ; Sutton et al. , 1998 ▶ ) 867 789 716 702 2.3 0.73 1.02 0.62 GPATase ( 1ecf ; Muchmore et al. , 1998 ▶ ) 992 318 191 129 2.3 0.82 1.30 0.48 Granulocyte ( 2gmf ; Rozwarski et al. , 1996 ▶ ) 241 117 87 76 2.3 0.62 1.04 0.50 VMP ( 1l8w ; Eicken et al. , 2002 ▶ ) 1141 654 621 528 2.3 0.76 1.01 0.61 Armadillo ( 3bct ; Huber et al. , 1997 ▶ ) 457 329 232 197 2.4 0.86 0.88 0.59 Cyanase ( 1dw9 ; Walsh et al. , 2000 ▶ ) 1560 710 462 364 2.4 0.82 1.30 0.47 Mev kinase ( 1kkh ; Yang et al. , 2002 ▶ ) 317 123 133 96 2.4 0.83 1.28 0.54 NSF D2 ( 1nsf ; Yu et al. , 1998 ▶ ) 247 110 52 45 2.4 0.84 0.78 0.56 1102B ( 1l2f ; Shin, Nguyen et al. , 2003 ▶ ) 344 118 137 79 2.5 0.78 1.49 0.49 AEP transaminase ( 1m32 ; Chen et al. , 2002 ▶ ) 2169 849 792 609 2.5 0.81 1.23 0.49 FLR ( 1bkj ; Tanner et al. , 1996 ▶ ) 460 209 64 45 2.5 0.77 1.74 0.41 P32 ( 1p32 ; Jiang et al. , 1999 ▶ ) 529 190 235 172 2.5 0.86 1.15 0.56 PSD-95 ( 1jxm ; Tavares et al. , 2001 ▶ ) 264 87 72 34 2.5 0.76 1.66 0.49 QAPRTase ( 1qpo ; Sharma et al. , 1998 ▶ ) 1704 737 525 399 2.5 0.71 1.27 0.51 RNase S ( 1rge ; Sevcik et al. , 1996 ▶ ) 192 23 32 11 2.5 0.65 2.16 0.34 Gene V ( 1vqb ; Skinner et al. , 1994 ▶ ) 86 0 26 0 2.6 0.74 2.19 0.27 Rab3A ( 1zbd ; Ostermeier Brnger, 1999 ▶ ) 301 110 104 89 2.6 0.82 1.03 0.55 GerE ( 1fse ; Ducros et al. , 2001 ▶ ) 384 251 179 145 2.7 0.70 1.07 0.60 CP synthase ( 1l1e ; Huang et al. , 2002 ▶ ) 534 220 186 150 2.8 0.75 0.99 0.54 Rh dehalogenase ( 1bn7 ; Newman et al. , 1999 ▶ ) 291 109 138 86 2.8 0.78 1.44 0.46 S-hydrolase ( 1a7a ; Turner et al. , 1998 ▶ ) 861 349 343 240 2.8 0.81 1.30 0.48 UT synthase ( 1e8c ; Gordon et al. , 2001 ▶ ) 990 306 293 180 2.8 0.78 1.46 0.45 1029B ( 1n0e ; Chen et al. , 2004 ▶ ) 1130 379 255 116 3.0 0.73 1.71 0.44 1038B ( 1lql ; Choi et al. , 2003 ▶ ) 1432 440 628 367 3.0 0.71 1.58 0.48 1071B ( 1nf2 ; Shin, Roberts et al. , 2003 ▶ ) 801 286 215 136 3.0 0.65 1.69 0.49 Synaptotagmin ( 1dqv ; Sutton et al. , 1999 ▶ ) 275 8 71 3 3.2 0.67 2.08 0.41 GroEL ( 1oel ; Braig et al. , 1995 ▶ ) 3668 1841 1443 1291 3.8 0.55 1.52 0.57

Publication Year: 2010


Rapid model building of beta-sheets in electron-density maps.

(2010) Acta Crystallogr D Biol Crystallogr 66

PubMed: 20179339 | PubMedCentral: PMC2827348 | DOI: 10.1107/S0907444910000302

Table 1 -Strand identification in experimental electron-density maps   Residues         Structure Total Strand Built Correct d min () Map quality (CC to model m... p) R.m.s.d. () Strandmap CC RNase P ( 1nz0 ; Kazantsev et al. , 2003 ▶ ) 416 88 18 11 1.5 0.53 1.90 0.30 1063B ( 1lfp ; Shin et al. , 2002 ▶ ) 243 57 42 33 1.7 0.68 1.58 0.41 Epsin ( 1edu ; Hyman et al. , 2000 ▶ ) 149 0 15 0 1.8 0.89 2.24 0.35 Isocitrate lyase ( 1f61 ; Sharma et al. , 2000 ▶ ) 836 98 161 67 1.8 0.65 1.75 0.42 MBP ( 1ytt ; Burling et al. , 1996 ▶ ) 227 61 60 33 1.8 0.89 1.48 0.39 P9 ( 1bkb ; Peat et al. , 1998 ▶ ) 136 73 59 50 1.8 0.81 1.02 0.48 Penicillopepsin ( 3app ; James Sielecki, 1983 ▶ ) 323 147 122 94 1.8 0.84 1.10 0.45 Myoglobin (Ana Gonzlez, personal communication) 154 0 17 0 1.9 0.73 3.34 0.24 ROP ( 1f4n ; Willis et al. , 2000 ▶ ) 108 0 20 0 1.9 0.84 2.80 0.25 1167B ( 1s12 ; Shin et al. , 2005 ▶ ) 370 108 93 69 2.0 0.72 1.50 0.47 CobD ( 1kus ; Cheong et al. , 2002 ▶ ) 355 56 80 32 2.0 0.80 1.97 0.35 NSF-N ( 1qcs ; Yu et al. , 1999 ▶ ) 195 83 60 42 2.0 0.80 1.50 0.37 Synapsin ( 1auv ; Esser et al. , 1998 ▶ ) 585 179 165 122 2.0 0.78 1.14 0.48 Tryparedoxin ( 1qk8 ; Alphey et al. , 1999 ▶ ) 143 33 39 21 2.0 0.79 1.87 0.37 PDZ ( 1kwa ; Daniels et al. , 1998 ▶ ) 174 66 36 30 2.1 0.67 1.41 0.43 Fusion complex ( 1sfc ; Sutton et al. , 1998 ▶ ) 867 0 32 0 2.3 0.73 2.95 0.41 GPATase ( 1ecf ; Muchmore et al. , 1998 ▶ ) 992 223 248 179 2.3 0.82 1.28 0.52 Granulocyte ( 2gmf ; Rozwarski et al. , 1996 ▶ ) 241 20 14 0 2.3 0.62 2.61 0.35 VMP ( 1l8w ; Eicken et al. , 2002 ▶ ) 1141 16 89 8 2.3 0.76 1.80 0.35 Armadillo ( 3bct ; Huber et al. , 1997 ▶ ) 457 0 38 0 2.4 0.86 2.66 0.33 Cyanase ( 1dw9 ; Walsh et al. , 2000 ▶ ) 1560 290 294 168 2.4 0.82 1.76 0.40 Mev kinase ( 1kkh ; Yang et al. , 2002 ▶ ) 317 77 91 62 2.4 0.83 1.46 0.47 NSF D2 ( 1nsf ; Yu et al. , 1998 ▶ ) 247 37 70 28 2.4 0.84 1.81 0.44 1102B ( 1l2f ; Shin, Nguyen et al. , 2003 ▶ ) 344 96 82 70 2.5 0.78 1.12 0.50 AEP transaminase ( 1m32 ; Chen et al. , 2002 ▶ ) 2169 354 423 264 2.5 0.81 1.46 0.42 FLR ( 1bkj ; Tanner et al. , 1996 ▶ ) 460 62 91 44 2.5 0.77 1.81 0.36 P32 ( 1p32 ; Jiang et al. , 1999 ▶ ) 529 144 154 115 2.5 0.86 1.58 0.51 PSD-95 ( 1jxm ; Tavares et al. , 2001 ▶ ) 264 68 69 47 2.5 0.76 1.42 0.46 QAPRTase ( 1qpo ; Sharma et al. , 1998 ▶ ) 1704 324 275 166 2.5 0.71 1.43 0.42 RNase S ( 1rge ; Sevcik et al. , 1996 ▶ ) 192 49 45 25 2.5 0.65 2.42 0.29 Gene V ( 1vqb ; Skinner et al. , 1994 ▶ ) 86 40 24 17 2.6 0.74 1.11 0.46 Rab3A ( 1zbd ; Ostermeier Brnger, 1999 ▶ ) 301 58 57 37 2.6 0.82 1.49 0.49 GerE ( 1fse ; Ducros et al. , 2001 ▶ ) 384 0 16 0 2.7 0.70 2.22 0.42 CP synthase ( 1l1e ; Huang et al. , 2002 ▶ ) 534 86 138 72 2.8 0.75 1.86 0.41 Rh dehalogenase ( 1bn7 ; Newman et al. , 1999 ▶ ) 291 53 67 37 2.8 0.78 1.71 0.42 S-hydrolase ( 1a7a ; Turner et al. , 1998 ▶ ) 861 135 247 83 2.8 0.81 1.86 0.37 UT synthase ( 1e8c ; Gordon et al. , 2001 ▶ ) 990 213 248 157 2.8 0.78 1.49 0.43 1029B ( 1n0e ; Chen et al. , 2004 ▶ ) 1130 232 267 139 3.0 0.73 1.36 0.49 1038B ( 1lql ; Choi et al. , 2003 ▶ ) 1432 483 472 399 3.0 0.71 1.32 0.54 1071B ( 1nf2 ; Shin, Roberts et al. , 2003 ▶ ) 801 184 232 143 3.0 0.65 1.39 0.54 Synaptotagmin ( 1dqv ; Sutton et al. , 1999 ▶ ) 275 87 49 29 3.2 0.67 1.39 0.42 GroEL ( 1oel ; Braig et al. , 1995 ▶ ) 3668 644 26 18 3.8 0.55 1.37 0.40

Publication Year: 2010


Rapid chain tracing of polypeptide backbones in electron-density maps.

(2010) Acta Crystallogr D Biol Crystallogr 66

PubMed: 20179340 | PubMedCentral: PMC2827349 | DOI: 10.1107/S0907444910000272

Table 1 Chain-tracing in experimental electron-density maps Structure d min (Å) Map quality (CC to model map using data to 3 Å) Residues Residues built C α r.m.s.d. (&#... 000c5;) Residues in secondary structure (%) CPU time (s) RNase P ( 1nz0 ; Kazantsev et al. , 2003 ▶ ) 1.5 0.53 416 284 2.53 8 14 1063B ( 1lfp ; Shin et al. , 2002 ▶ ) 1.7 0.68 243 132 1.98 17 7 Epsin ( 1edu ; Hyman et al. , 2000 ▶ ) 1.8 0.89 149 132 1.31 43 6 Isocitrate lyase ( 1f61 ; Sharma et al. , 2000 ▶ ) 1.8 0.65 836 754 1.59 42 81 MBP ( 1ytt ; Burling et al. , 1996 ▶ ) 1.8 0.89 227 194 1.41 69 9 P9 ( 1bkb ; Peat et al. , 1998 ▶ ) 1.8 0.81 136 128 1.61 76 9 Penicillopepsin ( 3app ; James & Sielecki, 1983 ▶ ) 1.8 0.84 323 279 1.58 41 10 Myoglobin (Ana Gonzales, personal communication) 1.9 0.73 154 139 1.96 5 10 ROP ( 1f4n ; Willis et al. , 2000 ▶ ) 1.9 0.84 108 107 2.07 60 4 1167B ( 1s12 ; Shin et al. , 2005 ▶ ) 2.0 0.72 370 254 1.77 42 10 CobD ( 1kus ; Cheong et al. , 2002 ▶ ) 2.0 0.80 355 331 1.73 32 18 NSF-N ( 1qcs ; Yu et al. , 1999 ▶ ) 2.0 0.80 195 162 1.57 40 8 Synapsin ( 1auv ; Esser et al. , 1998 ▶ ) 2.0 0.78 585 421 1.71 60 24 Tryparedoxin ( 1qk8 ; Alphey et al. , 1999 ▶ ) 2.0 0.79 143 142 1.67 47 6 PDZ ( 1kwa ; Daniels et al. , 1998 ▶ ) 2.1 0.67 174 130 1.65 50 7 Fusion complex ( 1sfc ; Sutton et al. , 1998 ▶ ) 2.3 0.73 867 643 1.98 14 141 GPATase ( 1ecf ; Muchmore et al. , 1998 ▶ ) 2.3 0.82 992 901 1.49 71 50 Granulocyte ( 2gmf ; Rozwarski et al. , 1996 ▶ ) 2.3 0.62 241 141 1.80 16 8 VMP ( 1l8w ; Eicken et al. , 2002 ▶ ) 2.3 0.76 1141 833 1.42 41 37 Armadillo ( 3bct ; Huber et al. , 1997 ▶ ) 2.4 0.86 457 369 1.21 59 23 Cyanase ( 1dw9 ; Walsh et al. , 2000 ▶ ) 2.4 0.82 1560 1506 1.71 55 62 Mev kinase ( 1kkh ; Yang et al. , 2002 ▶ ) 2.4 0.83 317 302 1.38 66 9 NSF D2 ( 1nsf ; Yu et al. , 1998 ▶ ) 2.4 0.84 247 243 1.59 49 11 1102B ( 1l2f ; Shin, Nguyen et al. , 2003 ▶ ) 2.5 0.78 344 308 1.45 56 22 AEP transaminase ( 1m32 ; Chen et al. , 2002 ▶ ) 2.5 0.81 2169 2045 1.32 71 95 FLR ( 1bkj ; Tanner et al. , 1996 ▶ ) 2.5 0.77 460 401 2.01 39 13 P32 ( 1p32 ; Jiang et al. , 1999 ▶ ) 2.5 0.86 529 475 1.38 71 13 PSD-95 ( 1jxm ; Tavares et al. , 2001 ▶ ) 2.5 0.76 264 231 1.46 53 13 QAPRTase ( 1qpo ; Sharma et al. , 1998 ▶ ) 2.5 0.71 1704 1209 1.53 35 69 RNase S ( 1rge ; Sevcik et al. , 1996 ▶ ) 2.5 0.65 192 133 2.06 42 7 Gene V ( 1vqb ; Skinner et al. , 1994 ▶ ) 2.6 0.74 86 74 1.52 65 4 Rab3A ( 1zbd ; Ostermeier & Brünger, 1999 ▶ ) 2.6 0.82 301 262 1.55 41 19 GerE ( 1fse ; Ducros et al. , 2001 ▶ ) 2.7 0.70 384 317 1.41 27 14 CP synthase ( 1l1e ; Huang et al. , 2002 ▶ ) 2.8 0.75 534 253 1.53 40 18 Rh dehalogenase ( 1bn7 ; Newman et al. , 1999 ▶ ) 2.8 0.78 291 270 1.42 56 9 S-hydrolase ( 1a7a ; Turner et al. , 1998 ▶ ) 2.8 0.81 861 813 1.62 41 43 UT synthase ( 1e8c ; Gordon et al. , 2001 ▶ ) 2.8 0.78 990 867 1.53 60 48 1029B ( 1n0e ; Chen et al. , 2004 ▶ ) 3.0 0.73 1130 1016 1.57 61 37 1038B ( 1lql ; Choi et al. , 2003 ▶ ) 3.0 0.71 1432 1308 1.39 70 114 1071B ( 1nf2 ; Shin, Roberts et al. , 2003 ▶ ) 3.0 0.65 801 760 1.63 67 62 Synaptotagmin ( 1dqv ; Sutton et al. , 1999 ▶ ) 3.2 0.67 275 199 2.55 19 29 GroEL ( 1oel ; Braig et al. , 1995 ▶ ) 3.8 0.55 3668 1960 1.98 14 247 Table 2 Comparison of model-building procedures Method Residues built (of 26651 possible residues in 42 experimental density-modified maps) R.m.s.d. (Å) Time (s) Residues per second trace_chain † 21428 1.61 1441 14.9 Helices–strands ‡ 12322 1.24 5331 2.3 RESOLVE § 19037 1.16 16933 1.1 phenix.autobuild ¶ 20601 0.95 155767 0.1 † trace_chain is the method in this paper (without optional assembly steps) with phenix.find_helices_strands and trace_chain=True.

Publication Year: 2010


Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion.

(2010) Nat Struct Mol Biol 17

PubMed: 20173762 | PubMedCentral: PMC2928146 | DOI: 10.1038/nsmb.1764

(c) Superposition of the crystal structures of SNARE-induced Ca 2− -bound (magenta and yellow) and Ca 2+ -free (blue, PDB ID 1DQV 20 ) Syt3 C2AB fragments.

Publication Year: 2010


Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation.

(2011) Nat Struct Mol Biol 18

PubMed: 21642968 | PubMedCentral: PMC3130798 | DOI: 10.1038/nsmb.2061

The C2AB-domain was simulated based on the crystal structure (PDB 1DQV) 50 .

Publication Year: 2011


Towards automated crystallographic structure refinement with phenix.refine.

(2012) Acta Crystallogr D Biol Crystallogr 68

PubMed: 22505256 | PubMedCentral: PMC3322595 | DOI: 10.1107/S0907444912001308

Impact of ADP refinement   The re-refinement of a synaptotagmin structure at 3.2 Å resolution (PDB entry 1dqv ; Sutton et al. , 1999 ▶ ) emphasizes the importance of us... ng a TLS parameterization not only as a way to reduce the number of refined parameters but more importantly to provide a more reasonable model for global domain motions (Urzhumtsev et al. , 2011 ▶ ).

Extracted from REMARK records of PDB file header Calculated with PHENIX from original PDB † PDB_REDO ‡ Re-refined in phenix.refine § Code ¶ d min () Data source R work / R free (%) R work / R free (%) RO (%) CS R work / R free (%) RO (%) CS R work / R free (%) RO (%) CS 1jl4 4.3 X-ray 42.0/45.3 34.2/37.0 0.74 40.0 23.9/31.4 0.74 25.8 24.2/30.9 0.92 13.3 2gsz 4.2 X-ray 34.3/40.6 31.0/36.1 1.33 37.1 34.3/39.9 1.33 37.1 25.8/32.7 0.98 25.7 1yi5 4.2 X-ray 33.1/37.8 30.3/33.9 2.79 17.6 24.1/31.1 2.86 15.9 25.9/28.5 0.98 15.5 2wjx 4.1 X-ray 29.0/35.4 33.7/37.0 0.28 24.5 33.8/36.7 0.28 24.6 28.5/31.9 0.28 11.8 1av1 4.0 X-ray 38.2/42.8 35.1/38.4 1.26 55.4 35.1/40.1 1.01 58.1 33.3/36.3 0.50 16.1 3bbw 4.0 X-ray 30.2/35.4 21.8/22.8 2.82 21.6 18.4/19.9 1.32 15.9 18.1/21.5 0.94 11.1 2i07 4.0 X-ray 27.3/32.3 26.8/28.7 2.04 24.9 22.5/28.5 1.84 20.4 21.5/26.4 0.79 14.6 3eob 3.6 X-ray 26.7/33.3 26.7/33.5 2.08 40.4 27.6/34.5 2.08 40.5 26.8/29.3 0.50 12.6 1dqv 3.2 X-ray 29.3/34.8 30.2/na †† 10.3 93.1 na na na 22.2/25.5 0.37 24.8 1c57 2.4 Neutron 27.0/30.1 30.0/33.9 0 6.2 na na na 20.4/25.7 0 11.2 1jmc 2.4 X-ray 21.2/33.0 20.1/31.6 1.69 31.0 21.5/28.9 1.69 14.6 22.0/27.2 1.27 16.4 1eic 1.4 X-ray 20.1/25.4 20.1/25.2 0.82 21.7 16.0/17.7 0.82 11.9 12.9/15.9 0.82 20.0 2elg 1.0 X-ray 23.2/24.7 22.85/na 0 7.3 14.1/16.9 0 2.4 14.1/16.0 0 7.3 1g2y 1.0 X-ray 19.5/19.8 19.7/19.0 0.89 10.0 16.1/17.5 0.89 8.6 14.4/15.3 0.89 15.5 2ppn 0.92 X-ray 20.9/19.9 20.4/19.8 0 8.1 15.4/16.0 0 8.6 13.3/14.7 0 14.6 ur0013 0.65 Neutron 9.5/na 9.1/na 0 0 na na na 7.8/9.6 0 0 † Calculated in PHENIX after applying resolution and cutoffs, as reported in the PDB file header.

Publication Year: 2012


Common exonic missense variants in the C2 domain of the human KIBRA protein modify lipid binding and cognitive performance.

(2013) Transl Psychiatry 3

PubMed: 23778582 | PubMedCentral: PMC3693407 | DOI: 10.1038/tp.2013.49

23 However, in contrast to synaptotagmin that contains two positionally flexible C2 domains (PDB ID: 1DQV), 24 , 25 the conformation of the C2 dimer of KIBRA is constrained through a cysteine bridge o... C771.

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4528800

T ( 2 ) L (deg 2 ) S (deg) 1dqv A 1 A 97 0.1777 0.0090 0.0044 1.4462 0.0160 0.2656 0.0467 0.0523 0.0566 0.0090 0.1306 0.0019 0.0160 1.2556 0.4713 0.1010 0.0032 0.0164 0.0044 0.0019 0.1372 0.2656 0.471... 0.8689 0.0090 0.0188 0.0560 B 1 B 97 0.1777 0.0090 0.0044 1.4462 0.0160 0.2656 0.0467 0.0523 0.0566 0.0090 0.1306 0.0019 0.0160 1.2556 0.4713 0.1010 0.0032 0.0164 0.0044 0.0019 0.1372 0.2656 0.4713 0.8689 0.0090 0.0188 0.0560 1exr A 2 A 30 0.0899 0.0040 0.0004 1.3491 0.3760 0.3971 0.0249 0.3537 0.0874 0.0040 0.1333 0.0058 0.3760 0.6103 0.3389 0.1275 0.0783 0.0144 0.0004 0.0058 0.0728 0.3971 0.3389 0.3698 0.0183 0.0542 0.0103 A 31 A 74 0.0925 0.0037 0.0041 0.3464 0.3638 0.2923 0.0220 0.0419 0.0793 0.0037 0.0673 0.0062 0.3638 0.3283 0.1212 0.0061 0.0018 0.1161 0.0041 0.0062 0.1119 0.2923 0.1212 0.3799 0.0041 0.0385 0.0009 A 75 A 84 0.2433 0.0144 0.0917 0.0736 0.0171 0.0565 0.4357 0.1151 0.2346 0.0144 0.2867 0.1720 0.0171 0.0068 0.0203 0.2521 0.3549 0.2041 0.0917 0.1720 0.1749 0.0565 0.0203 0.0336 0.3793 0.1499 0.0111 A 85 A 147 0.0747 0.0110 0.0066 0.6097 0.0786 0.1864 0.0180 0.1466 0.0378 0.0110 0.1384 0.0062 0.0786 0.6474 0.6233 0.0155 0.0872 0.0542 0.0066 0.0062 0.0673 0.1864 0.6233 0.9637 0.0440 0.1022 0.0852 4b3x A 1 A 65 0.4663 0.0991 0.0764 0.4738 0.0063 0.2318 0.0391 0.0307 0.4316 0.0991 0.5443 0.0321 0.0063 0.2120 0.0584 0.0587 0.1786 0.2003 0.0764 0.0321 0.5001 0.2318 0.0584 0.1312 0.3665 0.4293 0.0403 A 66 A 363 0.1649 0.0259 0.0184 0.8808 0.0912 0.1736 0.0345 0.0102 0.0661 0.0259 0.1422 0.0055 0.0912 0.9522 0.0972 0.1159 0.0222 0.0999 0.0184 0.0055 0.2028 0.1736 0.0972 1.6563 0.0424 0.1330 0.0237 Table 3 Examples of parameters of the elemental motions found from decomposition of the TLS matrices The parameters are given in the units used in this article, allowing an easy estimation of the corresponding atomic displacements.

Synaptotagmin   The crystals of synaptotagmin III (PDB entry 1dqv ; Sutton et al. , 1999 ▸ ) contain two copies of the molecule in the asymmetric unit.

T : t x , t y , t z () L : d x , d y , d z (rad) S : s x , s y , s z () tr( S ) 1dqv A 1 A 97 0.3455 0.3671 0.4172 0.01239 0.02044 0.02273 1.343 1.137 1.319 0 B 1 B 97 0.3634 0.3885 0.4166 0.01608 0.01753 0.03069 0.679 1.177 0.200 0 1exr A 2 A 30 0.1944 0.2663 0.2870 0.00000 0.01602 0.02182 0.000 2.951 3.408 >0 A 31 A 74 0.2110 0.2939 0.3068 0.00000 0.00860 0.01637 0.000 18.14 5.028 0 A 75 A 84 0.1692 0.4906 0.6598 0.00000 0.00000 0.00000 0.000 0.000 0.000 0 A 85 A 147 0.0002 0.2270 0 3078 0.00553 0.01418 0.02109 20.83 0.800 1.672 0 4b3x A 1 A 65 0.0994 0.6064 0.7116 0.00000 0.00825 0.01343 0.000 2.718 11.05 0 A 66 A 363 0.3306 0.4102 0.4413 0.01568 0.01720 0.02283 3.164 2.276 0.197 0

Yellow spheres in the 1dqv model show the reaction centres.

( a ) 1dqv model.

Publication Year: 2015