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PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

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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

Structures shown are aep-transaminase (PDB code 1m32; Chen et al. , 2002 ▶ ), armadillo (3bct; Huber et al. , 1997 ▶ ), 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 ▶ ), gene-5 (1vqb; Skinner et al. , 1994 ▶ ), gere (1fse; Ducros et al. , 2001 ▶ ), gpatase (1ecf; Muchmore et al. , 1998 ▶ ), group2-intron (1kxk; Zhang & Doudna, 2002 ▶ ), ic-lyase (1f61; Sharma et al. , 2000 ▶ ), lysozyme (unpublished results; CSHL Macromolecular Crystallography Course), mbp (1ytt; Burling et al. , 1996 ▶ ), mev-kinase (1kkh; Yang et al. , 2002 ▶ ), nsf-d2 (1nsf; Yu et al. , 1998 ▶ ), p32 (1p32; Jiang et al. , 1999 ▶ ), p9 (1bkb; Peat et al. , 1998 ▶ ), pdz (1kwa; Daniels et al. , 1998 ▶ ), psd-95 (1jxm; Tavares et al. , 2001 ▶ ), rab3a (1zbd; Ostermeier & Brunger, 1999 ▶ ), s-hydrolase (1a7a; Turner et al. , 1998 ▶ ), synapsin (1auv; Esser et al. , 1998 ▶ ), tryparedoxin (1qk8; Alphey et al. , 1999 ▶ ) and vmp (1l8w; Eicken et al. , 2002 ▶ ) ( b ) Structures determined using SAD: 1029B (1n0e; Chen et al. , 2004 ▶ ), 1038B (1lql; Choi et al. , 2003 ▶ ), 1063B (1lfp; Shin et al. , 2002 ▶ ), 1071B (1nf2; Shin, Roberts et al. , 2003 ▶ ), 1102B (1l2f; Shin, Nguyen et al. , 2003 ▶ ), 1167B (1s12; Shin et al. , 2005 ▶ ), rnase-p (1nz0; Kazantsev et al. , 2003 ▶ ), calmodulin (1exr; Wilson & Brunger, 2000 ▶ ), fusion-complex (1sfc; Sutton et al. , 1998 ▶ ), insulin (2bn3; Nanao et al. , 2005 ▶ ), myoglobin (A. Gonzales, personal communication), nsf-n (1qcs; Yu et al. , 1999 ▶ ), sec17 (1qqe; Rice & Brunger, 1999 ▶ ) and ut-synthase (1e8c; Gordon et al. , 2001 ▶ ).

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 (1nf2; 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 ▶ ).

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


Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.

(2009) Bioinformatics 25

PubMed: 19812110 | PubMedCentral: PMC2788923 | DOI: 10.1093/bioinformatics/btp576

RMSD of minimized full atomic structures Molecule Overall Helical Non-helical ID RMSD (Å) fragments fragments RMSD (Å) RMSD (Å) Validation structures (10 models) 1KXK 2.13 �... 0b1; 0.21 1.36 ± 0.44 2.41 ± 1.39 6TNA 2.81 ± 0.11 1.10 ± 0.09 3.02 ± 1.27 3CUL 3.06 ± 0.18 1.77 ± 0.82 2.48 ± 1.90 1GID 3.16 ± 0.08 2.03 ± 1.22 2.75 ± 1.45 1ZZN 2.79 ± 0.16 2.10 ± 0.74 2.56 ± 1.42 1Y0Q 2.76 ± 0.07 1.92 ± 0.68 2.50 ± 1.54 NAST tRNA models (50 models) Model A 8.39 ± 0.27 2.65 ± 0.71 4.13 ± 1.91 Model B 13.30 ± 0.31 3.08 ± 1.28 3.82 ± 1.51 Model C 15.99 ± 0.76 3.06 ± 1.13 4.19 ± 1.95 We report both overall RMSD values and separate values for helical and non-helical fragments.

Evaluation of minimized full atomic structures with MolProbity and the RCSB ADIT tool Molecule ID MolProbity RCSB ADIT Clashscore (goal=0) Percentile ( N =1784) Covalent bonds Covalent angles Crystal structure Best model Average (10 models) Crystal structure Best model Average (10 models) RMSD (Å) RMSD (degrees) Crystal Models Crystal Models 1KXK 14.03 3.33 8.54 ± 5.54 54 97 78.30 ± 22.53 0.006 0.017 0.9 2.8 6TNA 26.46 4.92 9.11 ± 4.54 19 94 76.60 ± 19.10 0.079 0.017 3.4 2.7 3CUL 7.67 6.11 8.56 ± 2.30 83 90 79.10 ± 10.81 0.007 0.020 1.0 3.2 1GID 35.78 13.31 23.21 ± 14.67 10 57 35.80 ± 18.36 0.009 0.031 0.9 3.4 1ZZN 32.67 15.29 29.46 ± 9.82 13 48 21.11 ± 16.00 0.008 0.032 1.1 3.6 1Y0Q 40.47 15.9 40.82 ± 17.72 8 46 13.60 ± 15.03 0.007 0.036 1.0 3.8 We give MolProbity Clashscores and percentiles for validation structures.

2.7 Validation using ideal backbones from crystal structures To validate our approach, we applied it to seven crystal structures of RNA molecules ranging in size from 70 to 244 residues: Yeast ai5g group II intron (‘Ai5gamma’, PDB ID 1KXK) 70 residues (Zhang and Doudna, 2002 ).

Publication Year: 2009


Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.

(2012) J Biomol NMR 53

PubMed: 22714631 | PubMedCentral: PMC3405240 | DOI: 10.1007/s10858-012-9642-5

In addition, beyond the bulge region (which is strongly influenced by packing effects and tertiary interactions), the stem and loop regions around the bulge better match the ai5γ-D5 (PDB: 1KXK... crystal structure than the previously published NMR structures.

Moreover, for regions outside the bulge region (which is strongly influenced by sequence, packing and tertiary interactions) the re-refined structures better match the ai5γ-D5 crystal structure (PDB: 1KXK).

The bulge conformation as reported in the earlier crystal structure of ai5γ-D5 (PDB: 1KXK) (Zhang and Doudna 2002 ) shows G26 forming a wobble pair with U9, while A24 and C25 are unpaired and opened away from the helix.

In addition, the lower helix regions of the re-refined structures are very similar to each other and better match the earlier crystal structure (PDB: 1KXK).

Publication Year: 2012


Automated 3D structure composition for large RNAs.

(2012) Nucleic Acids Res 40

PubMed: 22539264 | PubMedCentral: PMC3413140 | DOI: 10.1093/nar/gks339

Quality of predicted RNA 3D models a RNA PDB code and chain Strand length (nt) Accuracy b Precision c r.m.s.d. (Å) INF a ll INF c b p r.m.s.d. (Å) Hairpin    &#... 02003;2DR8 B 33 1.7 0.88 1.00 1.4     3OVA C 34 3.2 0.79 1.00 2.0 Hairpin, internal loop     1JBR D 31 4.4 0.74 0.98 2.7     2HW8 B 36 2.8 0.86 1.00 1.4     1ZHO B 38 2.0 0.83 0.99 1.1     3IAB R 46 11.0 0.72 0.88 1.2 Hairpin, internal loops     1I6U C 37 2.7 0.79 0.99 2.0     2PXL B 47 2.3 0.84 1.00 2.1     2VPL B 48 4.7 0.81 0.97 1.7     2PXB B 49 3.7 0.84 1.00 2.1     1MZP B 55 2.5 0.78 0.99 1.7     1KXK A 70 9.7 0.75 0.97 5.0 Three-way junction     1DK1 B 57 4.1 0.82 0.98 2.4     1MMS C 58 3.1 0.73 0.97 2.3     1UN6 E 61 4.0 0.80 0.88 2.2 Three-way junction (hammerhead)     2QUS A 69 3.8 0.81 0.96 1.6 Three-way junction (riboswitch)     3LA5 A 71 1.9 0.87 1.00 1.0     3D2V A 77 3.3 0.82 0.99 2.0 Three-way junction (GMP riboswitch)     3IWN A 93 3.9 0.75 0.97 2.3 Three-way junction (SRP)     2V3C M 96 10.0 0.76 0.94 3.0     1LNG B 97 6.6 0.77 0.99 2.6     1Z43 A 101 4.8 0.76 0.98 2.7     3NDB M 136 7.2 0.80 0.96 4.2 Three-way junction (5S rRNA)     3OFQ B 117 4.0 0.75 0.90 2.3     3OFR B 118 4.1 0.83 1.00 3.2     3KIR B 119 5.1 0.77 0.94 4.4     3I9E B 120 5.0 0.81 0.96 3.3     1VQO 9 122 3.3 0.84 1.00 2.6 Four-way junction (tRNA)     1EXD B 73 2.9 0.77 1.00 2.3     1U0B A 74 7.1 0.69 0.99 2.5     1FFY T 75 2.1 0.82 0.96 1.4     2J00 W 76 3.2 0.73 0.95 2.2 Four-way junction (riboswitch)     3IQP A 94 3.1 0.81 0.99 2.2 Five-way junction (tRNA)     3AM1 B 81 5.4 0.78 0.99 3.9     1WZ2 C 88 20.5 0.66 1.00 5.1     3ADB C 92 4.7 0.67 1.00 2.8 Pseudoknot     2QWY A 52 11.2 0.54 0.98 2.2 Pseudoknot (HDV ribozyme)     1CX0 B 72 2.7 0.83 0.97 1.6 P4–P6 ribozyme domain     2R8S R 159 15.2 0.76 0.99 7.9 M-box riboswitch     3PDR A 161 3.2 0.81 1.00 1.3 a Upon validation, all the 3D structure elements comprised by the respective crystal PDB structure were excluded from the dictionary.

Publication Year: 2012


Improving experimental phases for strong reflections prior to density modification.

(2013) Acta Crystallogr D Biol Crystallogr 69

PubMed: 24100322 | PubMedCentral: PMC3792643 | DOI: 10.1107/S0907444913018167

of non-H atoms Unit-cell parameters (Å, °) Case I: gene V protein (single-stranded DNA-binding protein; Skinner et al. , 1994 ▶ ) 1vqb C 2 2.6 682 a = 75.81, b = 27.92, c = 42.... 0, β = 103.1 Case II: RNA comprising domains 5 and 6 of the yeast ai5γ group II self-splicing intron (Zhang & Doudna, 2002 ▶ ) 1kxk P 6 1 22 3.5 1497 a = b = 91.68, c = 241.65, Case III: heterogeneous ribonucleoprotein A1 (Shamoo et al. , 1997 ▶ ) 1ha1 P 2 1 3.0 1338 a = 38.1, b = 44.0, c = 56.1, β = 94.8

Publication Year: 2013