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- PDB-2bhm: Crystal structure of VirB8 from Brucella suis -

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Basic information

Entry
Database: PDB / ID: 2bhm
TitleCrystal structure of VirB8 from Brucella suis
ComponentsTYPE IV SECRETION SYSTEM PROTEIN VIRB8Secretion
KeywordsBACTERIAL PROTEIN / BACTERIAL TYPE IV SECRETION
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
Type IV secretion system protein virB8
Similarity search - Component
Biological speciesBRUCELLA MELITENSIS BIOVAR SUIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å
AuthorsBayliss, R. / Baron, C. / Waksman, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structures of Two Core Subunits of the Bacterial Type Iv Secretion System, Virb8 from Brucella Suis and Comb10 from Helicobacter Pylori
Authors: Terradot, L. / Bayliss, R. / Oomen, C. / Leonard, G. / Baron, C. / Waksman, G.
History
DepositionJan 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
E: TYPE IV SECRETION SYSTEM PROTEIN VIRB8


Theoretical massNumber of molelcules
Total (without water)91,1015
Polymers91,1015
Non-polymers00
Water1,09961
1
A: TYPE IV SECRETION SYSTEM PROTEIN VIRB8

A: TYPE IV SECRETION SYSTEM PROTEIN VIRB8


Theoretical massNumber of molelcules
Total (without water)36,4402
Polymers36,4402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
MethodPQS
2
B: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
D: TYPE IV SECRETION SYSTEM PROTEIN VIRB8


Theoretical massNumber of molelcules
Total (without water)36,4402
Polymers36,4402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
E: TYPE IV SECRETION SYSTEM PROTEIN VIRB8


Theoretical massNumber of molelcules
Total (without water)36,4402
Polymers36,4402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)202.757, 202.757, 103.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsACCORDING TO THE AUTHORS OF THIS ENTRY, THE DIMER THAT ISGENERATED BY REMARK 350 BELOW MAY SHOW A LIKELY MODE OFSELF-ASSEMBLY OF VIRB8 WHICH IS KNOWN TO SELF-ASSOCIATETO FORM A LARGE COMPLEX.

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Components

#1: Protein
TYPE IV SECRETION SYSTEM PROTEIN VIRB8 / Secretion


Mass: 18220.145 Da / Num. of mol.: 5 / Fragment: RESIDUES 77-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRUCELLA MELITENSIS BIOVAR SUIS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 PLYSS / References: UniProt: Q7CEG3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.91 Å3/Da / Density % sol: 57.7 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→22.6 Å / Num. obs: 44402 / % possible obs: 98.8 % / Observed criterion σ(I): 6 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RESOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.4→26.6 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 2083 5 %RANDOM
Rwork0.2456 ---
obs0.2456 41354 98.4 %-
Solvent computationBsol: 34.2631 Å2 / ksol: 0.357974 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.731 Å20 Å20 Å2
2---4.731 Å20 Å2
3---9.462 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 0 61 5365
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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