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- PDB-3w2a: Crystal structure of VirB core domain complexed with the cis-acti... -

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Basic information

Entry
Database: PDB / ID: 3w2a
TitleCrystal structure of VirB core domain complexed with the cis-acting site upstream icsp promoter
Components
  • (DNA (31-mer)) x 2
  • Virulence regulon transcriptional activator VirB
KeywordsTRANSCRIPTION/DNA / ParS like DNA binding sites / ParB like protein / HTH DNA binding domain / 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 N-terminal 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 / MOLECULAR REPLACEMENT / Resolution: 2.775 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
DepositionNov 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Structure summary
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: DNA (31-mer)
C: DNA (31-mer)


Theoretical massNumber of molelcules
Total (without water)35,4533
Polymers35,4533
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.316, 39.828, 73.491
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Virulence regulon transcriptional activator VirB / Cell invasion regulator InvE


Mass: 16395.389 Da / Num. of mol.: 1 / Fragment: core domain, 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 (31-mer)


Mass: 9395.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA (31-mer)


Mass: 9662.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 64.88 %
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 16% PEG-400, 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: 0.97959 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2012
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.775→48.246 Å / Num. all: 23902 / Num. obs: 23902 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.68 % / Biso Wilson estimate: 65.815 Å2 / Rsym value: 0.09 / Net I/σ(I): 12.86
Reflection shellResolution: 2.78→2.94 Å / Redundancy: 5.76 % / Mean I/σ(I) obs: 2.31 / Num. unique all: 3942 / Rsym value: 0.761 / % possible all: 89.2

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERMRphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWB

3vwb


Resolution: 2.775→48.246 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7263 / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 32.74 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1194 5.02 %RANDOM
Rwork0.2415 ---
all0.2426 23902 --
obs0.2426 23806 97.84 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.102 Å2 / ksol: 0.256 e/Å3
Displacement parametersBiso max: 304.23 Å2 / Biso mean: 100.0706 Å2 / Biso min: 30.68 Å2
Baniso -1Baniso -2Baniso -3
1-38.2239 Å2-0 Å2-9.5862 Å2
2---20.5652 Å2-0 Å2
3----17.6587 Å2
Refinement stepCycle: LAST / Resolution: 2.775→48.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 943 0 41 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041991
X-RAY DIFFRACTIONf_angle_d0.9242882
X-RAY DIFFRACTIONf_chiral_restr0.043328
X-RAY DIFFRACTIONf_plane_restr0.003204
X-RAY DIFFRACTIONf_dihedral_angle_d26.205822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7755-2.88660.44281140.41992181229585
2.8866-3.01790.39041380.377225452683100
3.0179-3.1770.37151330.30262545267899
3.177-3.3760.28731340.25582525265998
3.376-3.63660.2781330.255525772710100
3.6366-4.00240.26211360.217325692705100
4.0024-4.58120.20171360.192125292665100
4.5812-5.77030.21911350.207125682703100
5.7703-48.25360.23371350.228125732708100
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)
10.90450.5477-1.93383.2007-0.54293.857-0.27450.1288-0.0864-0.8992-0.2234-0.7717-0.59730.18040.25940.526-0.09010.1620.46480.05270.48742.051212.87095.2327
25.1141-3.7842-0.58354.77382.73752.8589-0.14391.06730.4479-1.05050.50.1985-0.30620.1591-0.00180.9860.03490.07280.55720.06520.565238.49986.7145-4.3825
33.67250.0243-0.13024.82810.39723.85930.04310.23690.2059-0.58280.24510.33180.1655-0.1878-0.47080.4441-0.01230.06690.41390.05220.38438.69975.48266.227
41.50051.53932.19152.21820.74716.74170.27870.48281.07260.8571-0.2618-0.8394-0.26370.86160.14790.5439-0.0350.14650.42290.15060.467739.442817.129122.1213
52.6539-1.8601-2.21278.6936-3.13962.0679-0.2581-0.4178-0.4252-0.30120.1964-0.32680.89960.0696-0.19530.80970.220.12330.46560.03550.405238.15056.866320.0081
62.8602-0.44530.16124.1551-0.10861.90140.47560.61720.4818-0.8151-0.79091.91-0.9554-0.96620.30440.85180.16670.00860.6278-0.01470.677826.833319.395818.8485
72.09140.29645.19867.0731.69597.5125-0.736-0.36980.2392-0.091-0.4845-0.7455-0.3604-0.41710.03551.0745-0.3891.00730.05270.6387-1.023734.442920.535733.4333
84.5095-1.69035.96342.0184-0.65817.93361.0731-1.05160.5090.18760.6854-0.3379-0.061.1909-1.18951.81890.0738-0.04320.86760.07730.628242.586612.774538.5356
91.1134-1.72161.15475.046-0.25172.50350.4156-1.23210.4447-0.61370.1274-0.80890.34240.5456-0.11460.91510.07830.26890.5751-0.02750.487937.34219.184431.3337
106.8373-1.3985-4.66052.2971-0.29173.94330.3962-0.06210.381-0.00410.14911.49950.0501-1.5644-0.30811.2786-0.12530.08050.87250.16360.85524.693813.425828.2612
110.71180.13280.6160.02620.11110.5261-0.3159-0.1272-0.26290.3144-0.57950.867-0.2618-0.48650.60071.5413-0.5523-0.09292.9397-0.11422.9611.6248-3.9312-9.5106
122.9402-0.3646-1.51254.0378-1.47143.39310.2090.2582-0.5802-0.3680.13430.2771-0.21780.4615-0.22090.5588-0.1015-0.26050.491-0.04630.565336.6849-5.458610.5025
133.77411.62-0.96220.90270.52764.5675-0.3416-0.6577-0.93230.6540.37510.13940.6139-0.261-0.16781.74860.0742-0.43842.04790.16451.002253.8054-12.323535.8519
143.17350.2075-0.04484.41341.34965.15530.1616-0.2147-1.0920.03860.48520.28890.10090.7868-0.44150.47420.0985-0.12360.55070.10370.676641.7944-8.304617.6041
151.95-3.8039-5.18772.0046-5.7364.53370.46160.7192-0.2956-0.94681.7061-0.72911.0041-1.047-0.86992.48090.6867-1.94611.38850.5740.675218.40852.3324-10.208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 133:147)A133 - 147
2X-RAY DIFFRACTION2(CHAIN A AND RESID 148:157)A148 - 157
3X-RAY DIFFRACTION3(CHAIN A AND RESID 158:174)A158 - 174
4X-RAY DIFFRACTION4(CHAIN A AND RESID 175:184)A175 - 184
5X-RAY DIFFRACTION5(CHAIN A AND RESID 185:196)A185 - 196
6X-RAY DIFFRACTION6(CHAIN A AND RESID 197:216)A197 - 216
7X-RAY DIFFRACTION7(CHAIN A AND RESID 217:223)A217 - 223
8X-RAY DIFFRACTION8(CHAIN A AND RESID 224:229)A224 - 229
9X-RAY DIFFRACTION9(CHAIN A AND RESID 230:240)A230 - 240
10X-RAY DIFFRACTION10(CHAIN A AND RESID 241:246)A241 - 246
11X-RAY DIFFRACTION11(CHAIN B AND RESID 4:7)B4 - 7
12X-RAY DIFFRACTION12(CHAIN B AND RESID 8:22)B8 - 22
13X-RAY DIFFRACTION13(CHAIN B AND RESID 23:26)B23 - 26
14X-RAY DIFFRACTION14(CHAIN C AND RESID 3:20)C3 - 20
15X-RAY DIFFRACTION15(CHAIN C AND RESID 21:25)C21 - 25

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