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PDB ID Mentions in PubMed Central Article count: 10

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.

(2009) Nat Struct Mol Biol 16

PubMed: 19543291 | PubMedCentral: PMC2722044 | DOI: 10.1038/nsmb.1619

The search models used in the calculations were HEL (PDB code of 2VB1) 34 and the refined structure of unbound VLRB.2D. Final refinement statistics are summarized in Table 1 .

Publication Year: 2009


Polarizable atomic multipole X-ray refinement: application to peptide crystals.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19690373 | PubMedCentral: PMC2733883 | DOI: 10.1107/S0907444909022707

PDB code Atoms Reflections N symm Atoms × reflections × N symm × 10 −6 Direct (s) FFT (s) Direct/FFT SGFFT (s) Direct/SGFFT 1ejg 642 112209 2 144.1 49.9 28.1 1.8 7.3 6.... 2vb1 2544 187165 1 476.1 301.8 91.5 3.3 23.6 12.8 1fn8 4294 158550 1 680.8 245.1 45.8 5.4 12.4 19.8 1dy5 4835 159422 2 1541.6 505.6 37.0 13.7 9.7 52.1 1us0 6865 511265 2 7019.7 2346.2 162.3 14.5 42.3 55.5 Table 2 Refinement systems Molecule Space group and unit-cell parameters (Å, °) Non-H atoms H atoms Bonds d min (Å) Reflections YG 2 P 2 1 2 1 2 1 , a = 7.98, b = 9.54, c = 18.32 22 19 40 0.43 4766 P 2 A 4 P 2 1 2 1 2 1 , a = 10.13, b = 12.50, c = 19.50 35 36 72 0.37 24878 AYA + 3 waters P 2 1 , a = 8.12, b = 9.30, c = 12.53, β = 91.21 26 27 50 0.59 5019 AYA + ethanol P 2 1 , a = 8.85, b = 9.06, c = 12.36, β = 94.56 26 27 52 0.59 5258 Table 3 Refinement statistics and the relative AMOEBA potential energy per asymmetric unit are given for four small peptide crystals using the IAM, IAM–IAS, AMOEBA and AMOEBA–IAS scattering models In all cases, the lowest R free was found using the AMOEBA–IAS scattering model.

Publication Year: 2009


On the use of logarithmic scales for analysis of diffraction data.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19966414 | PubMedCentral: PMC2789003 | DOI: 10.1107/S0907444909039638

R (mvd, set 5) ( R PDB ) ( R ) ( R free ) ( R free R ) 0.67 2vb1 2vb1   0.0911 0.1090 0.1175 0.0089 0.670.76 1yk4 1r6j 2pve 0.1035 0.1199 0.1317 0.0121 0.760.87 2ol9 2h5c 2h5c 0.1158 0.1307 0.... 459 0.0153 0.871.00 1ob7 1rb9 1ixb 0.1281 0.1416 0.1601 0.0185 1.001.14 1iro 1iro 1z3n 0.1405 0.1525 0.1742 0.0217 1.141.31 2v9l 1n0q 2v9l 0.1528 0.1634 0.1884 0.0250 1.311.50 1hbz 2plz 1hbz 0.1651 0.1743 0.2026 0.0282 1.501.72 2ah2 6rxn 2pfg 0.1775 0.1851 0.2168 0.0314 1.721.97 1amk 2dya 2dya 0.1898 0.1960 0.2310 0.0346 1.972.25 2oh5 2oh5 2oh5 0.2021 0.2069 0.2452 0.0378 2.252.58 2oh7 1uvw 1uvw 0.2145 0.2178 0.2594 0.0410 2.582.95 5bna 1tre 1f4h 0.2268 0.2286 0.2736 0.0443 2.953.37 1bgj 1sv2 1ydz 0.2391 0.2395 0.2878 0.0475 3.373.86 2d3b 1gn3 2q3n 0.2515 0.2504 0.3020 0.0507 3.864.42 1aos 1veq 1veq 0.2638 0.2613 0.3162 0.0539 4.425.06 2rkj 1pgf 2rkj 0.2761 0.2721 0.3304 0.0571 5.065.80 3b5w 2b66 3b5x 0.2885 0.2830 0.3445 0.0603 5.806.63 2b9n 2b9n 3e3j 0.3008 0.2939 0.3587 0.0635 6.637.59 3c4y 3c4y 1yv0 0.3131 0.3048 0.3729 0.0668 7.598.69 2dh1 2dh1 2dh1 0.3255 0.3157 0.3871 0.0700 8.699.95 1vcr 1zbb 1vcr 0.3378 0.3265 0.4013 0.0732

Mean Mean Mode Mode difference set 1/set 2 0.67 2vb1 1ucs 124.8 178.4 152.9 149.0 130.7   0.670.76 1r6j 1yk4 88.1 253.0 133.5 109.1 96.8   0.760.87 1m40 1n55 50.6 180.7 81.7 79.8 71.7 0.01 0.871.00 2gkg 2rbk 39.0 106.1 57.0 58.4 53.1 0.06 1.001.14 2ofm 1rqw 26.2 113.1 45.2 42.8 39.3 0.16 1.141.31 2qj7 2dlb 18.9 90.7 31.9 31.3 29.1 0.00 1.311.50 1o6v 2ew0 12.8 54.3 21.8 22.9 21.5 0.00 1.501.72 2omq 2dga 8.1 56.6 15.8 16.8 15.9 0.00 1.721.97 3ins 2egx 5.6 40.5 11.8 12.3 11.8 0.02 1.972.25 1e0p 1zba 3.8 292.5 9.1 9.0 8.7 0.00 2.252.58 2ins 2izw 2.8 565.7 7.0 6.6 6.5 0.00 2.582.95 2p3c 1ng0 2.4 465.2 6.1 4.8 4.8 0.02 2.953.37 2vdt 1dwn 1.8 694.6 7.4 3.5 3.5 0.00 3.373.86 2dc3 1c8h 1.5 293.1 8.7 2.6 2.6 0.00 3.864.42 2gsz 1x35 1.1 73.0 3.9 1.9 1.9 0.01 4.425.06 1ye1 2g34 0.9 89.5 12.7 1.4 1.4   5.065.80 3b5x 2gp1 8.1 32.2 16.2 1.0 1.1   5.806.63 2zqp 2zqp 0.8 0.8 0.8 0.7 0.8   6.637.59 3c4y 1yv0 0.3 0.6 0.5 0.5 0.6   7.598.69 2dh1 2dh1 2.6 2.6 2.6 0.4 0.4   8.699.95 1vcr 2qzv 3.2 14.1 8.6 0.3 0.3   Table 3 Coefficients of the linear approximations Each function f ( d ) is presented as a linear function of the resolution logarithm, f ( d ) = a ln d + b .

Publication Year: 2009


Mining the protein data bank to differentiate error from structural variation in clustered static structures: an examination of HIV protease.

(2012) Viruses 4

PubMed: 22590675 | PubMedCentral: PMC3347031 | DOI: 10.3390/v4030348

The highest resolution structure of lysozyme in the PDB at the time of this writing, PDB ID 2vb1 [ 14 ], lists no B -factors lower than 2.15 Å 2 , so this was selected as the cut-off.

Publication Year: 2012


PubMed ID is not available.

Published in 2012

PubMedCentral: PMC3377366

A set of eight well refined high-resolution structures with data to resolutions in the range 0.7 to 1.2 Å and between 55 and 331 amino-acid residues in the asymmetric unit was used to ... est the enhanced rigid-bond restraint (PDB codes: 1b0y , 1lu0 , 1ok0 , 1rqw , 1us0 , 2cm5 , 2fdn and 2vb1 ).

Publication Year: 2012


Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

(2012) Acta Crystallogr D Biol Crystallogr 68

PubMed: 22868759 | PubMedCentral: PMC3413210 | DOI: 10.1107/S0907444912017453

of residues Bond-length r.m.s.d. () Bond-angle r.m.s.d. () Side-chain planarity r.m.s.d. () -Angle standard deviation () Clashes † Severe clashes ‡ Clashes † Severe clashes &#x... 2021; Reference 1byz 0.90 52 0.019 2.0 0.006 2.9 0 1 0 0 Priv et al. (1999 ▶ ) 1dy5 0.87 248 0.020 2.6 0.013 6.6 8 2 2 0 Esposito et al. (2000 ▶ ) 1i1w 0.89 303 0.041 2.9 0.016 6.4 1 2 0 0 Natesh et al. (2003 ▶ ) 1m40 0.85 263 0.014 2.6 0.009 6.1 1 0 0 0 Minasov et al. (2002 ▶ ) 1muw 0.86 386 0.016 2.5 0.010 8.2 18 3 7 0 Fenn et al. (2004 ▶ ) 1p9g 0.84 41 0.017 2.4 0.009 6.7 0 0 0 0 Xiang et al. (2004 ▶ ) 1ucs 0.62 64 0.014 2.2 0.010 5.3 0 1 0 0 Ko et al. (2003 ▶ ) 1vyr 0.90 364 0.017 2.3 0.012 5.8 0 0 0 0 Khan et al. (2004 ▶ ) 1yk4 0.69 52 0.022 2.7 0.011 5.7 2 3 0 0 Bnisch et al. (2005 ▶ ) 2b97 0.75 142 0.028 2.8 0.016 7.6 2 0 0 0 Hakanp et al. (2006 ▶ ) 2h5c 0.82 198 0.025 2.4 0.015 7.3 2 0 2 0 Fuhrmann et al. (2006 ▶ ) 2vb1 0.65 129 0.021 3.1 0.012 7.1 1 0 0 0 Wang et al. (2007 ▶ ) 2wur 0.90 236 0.034 3.3 0.016 6.6 10 5 7 0 Shinobu et al. (2010 ▶ ) 2xu3 0.90 220 0.011 1.4 0.007 5.7 1 1 1 1 Hardegger et al. (2011 ▶ ) 3a38 0.70 83 0.028 2.9 0.010 6.8 0 0 0 0 Takeda et al. (2010 ▶ ) 3g63 0.88 381 0.014 2.1 0.009 6.7 2 0 1 0 Liebschner et al. (2009 ▶ ) 3ip0 0.89 158 0.012 1.5 0.007 6.1 1 0 0 0 Blaszczyk et al. (2003 ▶ ) 3mi4 0.80 223 0.028 2.5 0.015 6.8 3 3 1 0 A. Brzuszkiewicz, M. Dauter Z. Dauter (unpublished work) Total   3543         52 21 21 1   Mean     0.021 2.5 0.011 6.4           Count per 100 residues         1.5 0.6 0.6 0.03   † A clash occurs when two atoms approach to within less than or equal to 0.8 times the sum of their van der Waals radii but greater than 0.7 times that sum.

Publication Year: 2012


On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses.

(2013) PLoS Comput Biol 9

PubMed: 24146608 | PubMedCentral: PMC3798281 | DOI: 10.1371/journal.pcbi.1003291

Furthermore, amyloid-like fibril forming peptide segments (Amylsegs) in PDB entries 1KCQ (human gelsolin domain 2), 2D4F (human β-microglobulin), and 2VB1 (hen egg-white lysozyme), are highly ... onserved among their homologues at both sequence identities (50% and 80%).

PDB entries for these proteins are 1FUK (C-terminal domain of yeast initiation factor 4A), 1JEO (Hypothetical protein MJ1247 from Methanococcus jannaschii ), 1KCQ (Human Gelsolin Domain 2), 1OW1 (SPOC domain of human transcriptional factor SHARP), 1SK7 (Hypothetical protein pa-HO from Pseudomonas aeruginosa ), 1Z77 (Transcriptional regulator (tetR family) from Thermotoga maritima ), 2D4F (Human β-microglobulin), 2VB1 (Hen Egg White Lysozyme) and 3NR5 (Human RNA polymerase III transcription repressor Maf1).

Publication Year: 2013


The active site of hen egg-white lysozyme: flexibility and chemical bonding.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24699657 | PubMedCentral: PMC3975892 | DOI: 10.1107/S1399004714001928

Computational details   X-ray diffraction data of HEWL without substrate, as deposited in the PDB (PDB entry 2vb1 ; Wang et al. , 2007 ▶ ; Table 1 ▶ ), were employed for struct... re refinements of the IAM and of a database-based multipole model.

The structure model of HEWL published by Wang et al. (2007 ▶ ) (PDB entry 2vb1 ) was employed as the starting model for the IAM refinement.

Table 1 Crystallographic data of hen egg-white lysozyme (PDB entry 2vb1 ; Wang et al. , 2007 ▶ ) Space group P 1 Z 1 a (Å) 27.07 b (Å) 31.25 c (Å) 33.76 α (°) 87.98 β (°) 108.00 γ (°) 112.11 V (Å 3 ) 25057.0 F (000) 10268.0 T (K) 100 Wavelength (Å) 0.65 [sin(θ)/λ] max (Å −1 ) 0.77 d min (Å) 0.65 pH 4.7 Multiplicity 7.1 R merge (%) 4.00 Completeness (%) 97.6 Unique reflections (observed/all) 166259/187165 R all (%) 8.39 IAM before elongation of bond lengths †     R F [ F obs with | I obs − I calc |/σ( I obs ) < 45/all reflections] (%) 8.39/8.54   R wF [ F obs with | I obs − I calc |/σ( I obs ) < 45/all reflections] (%) 10.19/10.80 Final IAM †   R F [ F obs with | I obs − I calc |/σ( I obs ) < 45/all reflections] (%) 8.39/8.54   R wF [ F obs with | I obs − I calc |/σ( I obs ) < 45/all reflections] (%) 10.19/10.80 ELMAM2 model †   R F [ F obs with | I obs − I calc |/σ( I obs ) < 45] (%) 8.07   R wF [ F obs with | I obs − I calc |/σ( I obs ) < 45] (%) 9.88 † Agreement indices from the IAM and the ELMAM2 model are from the present work.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4403875

g004 Fig 4 The appearance of electron density as a function of the nominal resolution of the experimental crystallographic data, (adapted from similar figure for the N-terminal fragment (Lys1—... al2—Phe3) of triclinic lysozyme (PDB: 2vb1) from Wlodawer et al. [ 33 ] for which permission to reproduce by the journal was not granted).

Publication Year: 2015


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4498469

Superimposition with monoclinic (PDB IDs: 2VB1, 1PS5), triclinic (1LKS), hexagonal (2FBB), orthorhombic (132L) and tetragonal (1IEE, 4B4E) HEWL structures revealed almost perfect structural matches, t... us indicating that the protein in general is very stable towards conformational changes (RMSD [residues] =0.35–0.43 Å; RMSD [Cα] =0.25–0.40 Å); only two loops (Cys64–Leu75 and Asp101–Asn103) showed slightly variable conformations.

Publication Year: 2014