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PDB ID Mentions in PubMed Central Article count: 1

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Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes.

(2013) Nucleic Acids Res 41

PubMed: 23985969 | PubMedCentral: PMC3905869 | DOI: 10.1093/nar/gkt748

Data collection and refinement statistics Parameter VirB core (SeMet derivative)/ icsb (DNA with 5-BRU modifications) (PDB ID: 3VWB) VirB core/ icsb (native DNA) (PDB ID: 3W3C) VirB core/ icsp (native... DNA) (PDB ID: 3W2A) Data collection     Space group P2 1 2 1 2 P2 1 2 1 2 C2     Cell dimensions     a, b, c (Å) 57.32, 163.05, 39.57 56.14, 163.40, 39.67 176.32, 39.83, 73.49     α,β,γ (°) 90.00, 90.00, 90.00 90.00, 90.00, 90.00 90.00, 90.00, 90.00     X ray source SLS BEAMLINE X06DA SSRF BEAMLINE BL17U SLS BEAMLINE X06DA     Wavelength (Å) 0.9792 (Se peak) 1.54001 0.9796 (Se peak)     Data range (Å) 46.89-2.42 40.85-2.43 48.25-2.78     Reflections unique 27467 13931 23902      R sym a (last shell) 0.067 (0.768) 0.049 (0.254) 0.090 (0.761)      I /σ I 21.56 (2.43) 20.49 (4.77) 12.86 (2.31)     Completeness (%) (last shell) 99.8 (98.8) 96.6 (95.8) 98.1 (89.2)     Redundancy (last shell) 7.77 (7.54) 4.95 (3.97) 6.68 (5.76) Refinement     Resolution range (Å) 46.89–2.42 40.85–2.43 48.25–2.78     Reflections (non-anomalous), cut-off, cross validation 27 362 (14 781), F>1.99, 1358 13 893 (13 893), F>1.88, 694 23 902 (12 578), F>2.0, 1194      R work b / R free c (last shell) 0.2370/0.2710 (0.3640/0.3901) 0.2640/0.2797 (0.3532/0.3778 0.2415/0.2624 (0.4199/0.4428) Atoms     Non-hydrogen protein atoms 2053 2061 1904     Protein 903 931 920     DNA 1088 1060 943     Solvent 62 70 41      B -factors average (Å 2) 65.76 60.1 96.03     Protein (Å 2 ) 53.25 48.9 74.13     DNA (Å 2 ) 77.39 71.3 118.99     Solvent (Å 2 ) 43.32 41.0 59.59     r.m.s.d     Bond lengths (Å) 0.004 0.003 0.004     Bond angles (°) 0.979 0.749 0.924 Validation     MolProbity score 2.11, 90th percentile d 1.76, 98th percentile d 2.44, 93rd percentile d     Clashscore, all atoms 14.36 7.79 18.7     % Poor rotamers 1.90 1.90 1.94     % residues in favored regions, allowed regions, outliers in Ramachandran plot 96.5, 2.6, 0.9 97.4, 0.9, 1.75 92.9, 6.2, 0.9 a R sym = ∑ hkl ∑ j |I hkl,j − I hkl |/∑ hkl ∑ j I hkl,j , where I hkl is the average of symmetry-related observations of a unique reflection.

ACCESSION CODES The atomic coordinates and structure factors have been deposited in the Protein Data Bank with the accession codes 3VWB, 3W3C and 3W2A.

Publication Year: 2013