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- PDB-3vwb: Crystal structure of VirB core domain (Se-Met derivative) complex... -

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Basic information

Entry
Database: PDB / ID: 3vwb
TitleCrystal structure of VirB core domain (Se-Met derivative) complexed with the cis-acting site (5-BRU modifications) upstream icsb promoter
Components
  • (DNA (26-MER)) x 2
  • Virulence regulon transcriptional activator virB
KeywordsTRANSCRIPTION/DNA / HTH DNA binding motif / dsDNA / Palindromic DNA sequence / ParB like / HTH DNA-binding motif / transcriptional activator / sequence specific dsDNA binding / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


ParB protein family, C-terminal / ParB family / Arc Repressor Mutant, subunit A - #2830 / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Virulence regulon transcriptional activator VirB
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.416 Å
AuthorsGao, X.P. / Waltersperger, S. / Wang, M.T. / Cui, S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes
Authors: Gao, X.P. / Zou, T.T. / Mu, Z.X. / Qin, B. / Yang, J. / Waltersperger, S. / Wang, M.T. / Cui, S. / Jin, Q.
History
DepositionAug 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references / Structure summary
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virulence regulon transcriptional activator virB
C: DNA (26-MER)
B: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)32,3573
Polymers32,3573
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-14 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.321, 163.051, 39.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Virulence regulon transcriptional activator virB / Cell invasion regulator invE


Mass: 16254.703 Da / Num. of mol.: 1 / Fragment: UNP residues 129-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 301 / Gene: virB / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P0A247
#2: DNA chain DNA (26-MER)


Mass: 8004.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA with two internal Br-dU labels
#3: DNA chain DNA (26-MER)


Mass: 8097.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.95 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M MgCl2, 0.1M Sodium Acetate, 22% PEG400, 3%(v/v) dimethyl sulfoxide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 5, 2011
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.416→46.891 Å / Num. all: 27467 / Num. obs: 27467 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.77 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.56
Reflection shellResolution: 2.42→2.56 Å / Redundancy: 7.54 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.43 / Num. unique all: 4363 / % possible all: 98.8

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHELXDphasing
SHELXEmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.416→46.891 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7987 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.83 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1358 4.96 %RANDOM
Rwork0.2353 ---
all0.2371 27467 --
obs0.2371 27362 99.58 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL. / Bsol: 31.73 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 190.73 Å2 / Biso mean: 68.9097 Å2 / Biso min: 13.81 Å2
Baniso -1Baniso -2Baniso -3
1-14 Å2-0 Å2-0 Å2
2---7.5335 Å2-0 Å2
3----6.4665 Å2
Refinement stepCycle: LAST / Resolution: 2.416→46.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 1060 0 62 2053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042144
X-RAY DIFFRACTIONf_angle_d0.9793103
X-RAY DIFFRACTIONf_chiral_restr0.046351
X-RAY DIFFRACTIONf_plane_restr0.003214
X-RAY DIFFRACTIONf_dihedral_angle_d27.192868
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4161-2.50250.391330.36412588272198
2.5025-2.60270.36141350.317926052740100
2.6027-2.72110.27381360.290625832719100
2.7211-2.86460.32291380.261826382776100
2.8646-3.0440.33441360.270426192755100
3.044-3.2790.25981340.24182556269099
3.279-3.60880.28751400.243925942734100
3.6088-4.13080.26581370.224525972734100
4.1308-5.20330.2461310.208626132744100
5.2033-46.89950.2241380.192126112749100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0208-0.01580.00540.0203-0.00740.00190.0031-0.0072-0.01-0.0148-0.0218-0.0101-0.02210.0034-00.9949-0.08890.20261.13450.05641.066358.50862.202-10.981
20.0071-0.0015-0.00550.00350.00090.0040.05780.0346-0.0589-0.0338-0.0325-0.0672-0.03780.0170.00320.1660.00880.03470.4132-0.00640.322956.069156.6188-14.2223
30.0408-0.0220.00480.0231-0.01580.01720.00960.0124-0.0351-0.03010.03740.06980.01040.10570.00410.20860.05990.06270.477-0.06870.26860.554844.2825-14.1235
40.0001-0.0128-0.01440.0728-0.06680.12860.0129-0.14330.0241-0.1662-0.047-0.1001-0.11490.1516-0.08880.20470.0282-0.0380.417-0.0640.224252.063753.658-12.369
50.0201-0.0051-0.0090.0040.01670.01140.0358-0.1683-0.04890.2067-0.0601-0.0151-0.0605-0.0244-0.00010.2568-0.0272-0.0030.5047-0.06830.298141.838952.5316-15.2894
60.01270.01420.00660.01530.00450.0073-0.01810.1072-0.0577-0.09470.0031-0.01360.00740.0204-0.10830.17130.1384-0.22430.5272-0.11580.112532.450859.84-24.8152
70.002-0.0014-0.0020.0034-0.00410.00940.0099-0.00340.0781-0.02830.03290.0387-0.0478-0.0093-00.46040.1760.15140.483-0.17620.640833.916671.4215-12.5223
80.0064-0.01670.00710.05280.00730.0406-0.0605-0.00460.0246-0.0124-0.01920.01320.063-0.0585-0.01570.29260.1809-0.04860.7664-0.14560.282832.932360.6065-13.2379
90.00250.0003-0.00140.0043-0.00010.0006-0.03130.0105-0.01950.0396-0.01150.0304-0.0104-0.0176-00.82720.08790.23220.6671-0.0020.563329.346452.0149-15.6255
100.0041-0.0034-0.00110.00960.00380.00030.019-0.0817-0.0320.0137-0.00320.0613-0.0371-0.0819-0.00011.2728-0.16770.19890.587-0.04961.399641.722320.0122-4.7936
110.0782-0.02550.02320.0149-0.03830.0564-0.1463-0.009-0.27360.2188-0.0625-0.03740.3103-0.1224-0.03120.3066-0.01560.03650.2419-0.09840.339649.894838.8347-1.5178
120.29190.1192-0.09060.0815-0.09660.11460.0167-0.36590.67820.2129-0.42150.2711-0.8303-0.1494-0.29041.26130.0463-0.0458-0.2726-0.1980.630845.062274.50488.025
130.00850.0455-0.0250.2360.06540.1757-0.15270.02610.58610.2017-0.1798-0.1416-0.251-0.1849-0.39091.44560.33570.0559-0.2647-0.24490.854242.811183.9027.2545
140.0830.0586-0.03930.0293-0.05260.0952-0.1098-0.0144-0.2025-0.0032-0.1237-0.03080.28870.0825-0.02180.52480.0090.09670.2195-0.04340.315949.239843.7899-0.8431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 131:132 )A131 - 132
2X-RAY DIFFRACTION2( CHAIN A AND RESID 133:141 )A133 - 141
3X-RAY DIFFRACTION3( CHAIN A AND RESID 142:153 )A142 - 153
4X-RAY DIFFRACTION4( CHAIN A AND RESID 154:184 )A154 - 184
5X-RAY DIFFRACTION5( CHAIN A AND RESID 185:208 )A185 - 208
6X-RAY DIFFRACTION6( CHAIN A AND RESID 209:224 )A209 - 224
7X-RAY DIFFRACTION7( CHAIN A AND RESID 225:234 )A225 - 234
8X-RAY DIFFRACTION8( CHAIN A AND RESID 235:241 )A235 - 241
9X-RAY DIFFRACTION9( CHAIN A AND RESID 242:246 )A242 - 246
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:4 )B1 - 4
11X-RAY DIFFRACTION11( CHAIN B AND RESID 5:13 )B5 - 13
12X-RAY DIFFRACTION12( CHAIN B AND RESID 14:26 )B14 - 26
13X-RAY DIFFRACTION13( CHAIN C AND RESID 1:13 )C1 - 13
14X-RAY DIFFRACTION14( CHAIN C AND RESID 14:26 )C14 - 26

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