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- PDB-3w3c: Crystal structure of VirB core domain complexed with the cis-acti... -

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Basic information

Entry
Database: PDB / ID: 3w3c
TitleCrystal structure of VirB core domain complexed with the cis-acting site upstream icsb promoter
Components
  • (DNA (26-MER)) x 2
  • Virulence regulon transcriptional activator VirB
KeywordsTRANSCRIPTION/DNA / HTH DNA binding motif / PROTEIN-DNA COMPLEX / ParB box-A like sequence / ParB like fold / 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: 2.431 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
DepositionDec 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,2273
Polymers32,2273
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-29 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.140, 163.400, 39.670
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): Rosetta DE3 / References: UniProt: P0A247
#2: DNA chain DNA (26-MER)


Mass: 8097.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA (26-MER)


Mass: 7875.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.3
Details: 0.1M MgCl2, 0.1M Sodium Acetate, 30% PEG400, 8%(v/v)1,3-Butanediol, pH 4.3, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.54001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54001 Å / Relative weight: 1
ReflectionResolution: 2.43→40.85 Å / Num. all: 13931 / Num. obs: 13895 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.95 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 20.49
Reflection shellResolution: 2.43→2.58 Å / Redundancy: 3.97 % / Mean I/σ(I) obs: 4.77 / Num. unique all: 2174 / Rsym value: 0.254 / % possible all: 95.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERfor MRphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 3VWB

3vwb


Resolution: 2.431→40.85 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7913 / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.88 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 694 5 %RANDOM
Rwork0.264 ---
obs0.2647 13893 96.31 %-
all-13893 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.72 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 146.18 Å2 / Biso mean: 59.666 Å2 / Biso min: 10.37 Å2
Baniso -1Baniso -2Baniso -3
1-11.0965 Å2-0 Å2-0 Å2
2---7.1143 Å2-0 Å2
3----3.9822 Å2
Refinement stepCycle: LAST / Resolution: 2.431→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 1060 0 70 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022134
X-RAY DIFFRACTIONf_angle_d0.7483101
X-RAY DIFFRACTIONf_chiral_restr0.036351
X-RAY DIFFRACTIONf_plane_restr0.003212
X-RAY DIFFRACTIONf_dihedral_angle_d25.488882
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4314-2.61910.37781360.35322583271997
2.6191-2.88260.35791420.318126862828100
2.8826-3.29950.28741400.2912695283599
3.2995-4.15640.29351250.28432367249287
4.1564-40.85570.22451510.20582868301999
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)
10.0452-0.00860.05050.0187-0.04270.1317-0.0433-0.2066-0.00880.0741-0.02250.076-0.141-0.1382-0.00450.2134-0.0070.03210.43410.03330.257-30.1676-30.813832.8952
20.0767-0.0320.02790.215-0.02830.15080.04890.23390.0360.094-0.10340.0714-0.22450.0617-0.12120.1886-0.0668-0.04440.39650.08920.1426-20.5265-25.277931.9355
30.3417-0.1092-0.16460.04240.06780.107-0.18120.0068-0.0742-0.00310.0561-0.0994-0.03090.1742-0.21130.2558-0.0903-0.11540.49150.09510.2456-6.379-23.148338.2605
40.00550.02020.010.0680.03270.0156-0.00520.0018-0.00560.01020.00430.00060.00750.01010.00041.2574-0.11410.10411.0956-0.03381.4618-0.2424-29.75836.7095
50.12880.07790.12780.07940.14250.2878-0.0574-0.0632-0.0399-0.1581-0.1709-0.04790.07440.0254-0.20070.31410.00090.08520.14770.03560.3095-19.1836-38.259919.3835
60.05970.0149-0.01410.0127-0.01730.04050.1139-0.12990.1323-0.0498-0.1189-0.0609-0.05080.09580.00381.4484-0.03380.00050.40920.17311.1304-12.19323.018210.7374
70.0207-0.028-0.05770.0710.03960.27150.03530.00620.0672-0.0717-0.06070.04910.03170.11470.07260.9445-0.51080.0525-0.18180.25741.121-13.93414.073811.9461
80.0639-0.0678-0.10580.04690.08820.14320.04010.0366-0.1453-0.2049-0.16180.10480.02360.178500.3682-0.00590.04710.24610.04280.3462-19.844-35.806120.5745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 131:156)A131 - 156
2X-RAY DIFFRACTION2(CHAIN A AND RESID 157:193)A157 - 193
3X-RAY DIFFRACTION3(CHAIN A AND RESID 194:242)A194 - 242
4X-RAY DIFFRACTION4(CHAIN A AND RESID 243:246)A243 - 246
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:19)B1 - 19
6X-RAY DIFFRACTION6(CHAIN B AND RESID 20:26)B20 - 26
7X-RAY DIFFRACTION7(CHAIN C AND RESID 1:12)C1 - 12
8X-RAY DIFFRACTION8(CHAIN C AND RESID 13:26)C13 - 26

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