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- PDB-5jbs: Conformational changes during monomer-to-dimer transition of Bruc... -

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Basic information

Entry
Database: PDB / ID: 5jbs
TitleConformational changes during monomer-to-dimer transition of Brucella suis VirB8
ComponentsType IV secretion system protein virB8
KeywordsTRANSPORT PROTEIN / M012R-VirB8
Function / homology
Function and homology information


protein secretion by the type IV secretion system / identical protein binding / plasma membrane
Similarity search - Function
VirB8 protein / Type IV secretion system protein VirB8/PtlE / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Type IV secretion system protein virB8
Similarity search - Component
Biological speciesBrucella suis biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsArya, T. / Sharifahmadian, M. / Sygusch, J. / Baron, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-84239 Canada
CitationJournal: To Be Published
Title: NMR analyses, X-ray crystallography and small-molecule probing reveal conformational shifts during monomer-to-dimer transition of Brucella suis VirB8
Authors: Arya, T. / Sharifahmadian, M. / Sygusch, J. / Baron, B.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type IV secretion system protein virB8
B: Type IV secretion system protein virB8
C: Type IV secretion system protein virB8
D: Type IV secretion system protein virB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,20315
Polymers63,7944
Non-polymers1,40911
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-2 kcal/mol
Surface area26680 Å2
Unit cell
Length a, b, c (Å)67.503, 78.723, 70.840
Angle α, β, γ (deg.)90.00, 111.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Type IV secretion system protein virB8


Mass: 15948.614 Da / Num. of mol.: 4 / Mutation: M102R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis biovar 1 (strain 1330) (bacteria)
Strain: 1330 / Gene: virB8, BRA0062, BS1330_II0062 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CEG3

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1 M Tris/HCl pH 6.8, 18% PEG-MME 2000 / PH range: 6.6-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→42.2 Å / Num. obs: 48835 / % possible obs: 97 % / Redundancy: 3.5 % / Net I/σ(I): 2.4

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Processing

SoftwareName: REFMAC / Version: 5.8.0123 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→42.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.374 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24097 2497 5.1 %RANDOM
Rwork0.19091 ---
obs0.19347 46338 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.119 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å21.94 Å2
2---3.63 Å20 Å2
3---3.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 88 321 4562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024343
X-RAY DIFFRACTIONr_bond_other_d0.0020.023970
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9545882
X-RAY DIFFRACTIONr_angle_other_deg1.06939138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2895515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0323.604197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78915687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0571528
X-RAY DIFFRACTIONr_chiral_restr0.1080.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9414.3822084
X-RAY DIFFRACTIONr_mcbond_other3.9354.3812083
X-RAY DIFFRACTIONr_mcangle_it5.4126.5222591
X-RAY DIFFRACTIONr_mcangle_other5.4116.5242592
X-RAY DIFFRACTIONr_scbond_it4.7275.012259
X-RAY DIFFRACTIONr_scbond_other4.7175.012259
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0317.2993292
X-RAY DIFFRACTIONr_long_range_B_refined9.53536.9655248
X-RAY DIFFRACTIONr_long_range_B_other9.52736.785178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 157 -
Rwork0.311 3024 -
obs--85.19 %

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