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- PDB-4mei: Crystal structure of a VirB8 Type IV secretion system machinery s... -

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Basic information

Entry
Database: PDB / ID: 4mei
TitleCrystal structure of a VirB8 Type IV secretion system machinery soluble domain from Bartonella tribocorum
ComponentsVirB8 protein
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / transmembrane protein / type IV secretion system / T4SS
Function / homology
Function and homology information


protein secretion by the type IV secretion system / endomembrane system / 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 speciesBartonella tribocorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: MBio / Year: 2015
Title: Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems.
Authors: Gillespie, J.J. / Phan, I.Q. / Scheib, H. / Subramanian, S. / Edwards, T.E. / Lehman, S.S. / Piitulainen, H. / Rahman, M.S. / Rennoll-Bankert, K.E. / Staker, B.L. / Taira, S. / Stacy, R. / ...Authors: Gillespie, J.J. / Phan, I.Q. / Scheib, H. / Subramanian, S. / Edwards, T.E. / Lehman, S.S. / Piitulainen, H. / Rahman, M.S. / Rennoll-Bankert, K.E. / Staker, B.L. / Taira, S. / Stacy, R. / Myler, P.J. / Azad, A.F. / Pulliainen, A.T.
History
DepositionAug 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: VirB8 protein


Theoretical massNumber of molelcules
Total (without water)20,8371
Polymers20,8371
Non-polymers00
Water25214
1
A: VirB8 protein

A: VirB8 protein


Theoretical massNumber of molelcules
Total (without water)41,6752
Polymers41,6752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1370 Å2
ΔGint-10 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.540, 61.540, 126.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein VirB8 protein


Mass: 20837.367 Da / Num. of mol.: 1 / Fragment: UNP residues 51-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella tribocorum (bacteria) / Strain: CIP 105476 / Gene: BT_1695, virB8 / Production host: Escherichia coli (E. coli) / References: UniProt: A9IWN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BatrA.18388.b.B2.PS01799 at 3.84 mg/mL against JCSG+ F10 1.1 M Na Malonate, 0.1 M Hepes pH 7.0, 0.5% Jeffamine ED2001 with 20% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: BatrA.18388.b.B2.PS01799 at 3.84 mg/mL against JCSG+ F10 1.1 M Na Malonate, 0.1 M Hepes pH 7.0, 0.5% Jeffamine ED2001 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 244429f10, unique puck ID jcp2-9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 6185 / Num. obs: 6166 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 56.293 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.85-2.920.5893.864091450100
2.92-30.4984.733828431100
3-3.090.3616.53709416100
3.09-3.190.268.693590404100
3.19-3.290.19111.333391386100
3.29-3.410.15714.063438392100
3.41-3.540.12117.233192370100
3.54-3.680.10220.373068355100
3.68-3.840.08224.3307735699.7
3.84-4.030.06927.472785324100
4.03-4.250.05732.112639315100
4.25-4.510.04538.162499298100
4.51-4.820.04339.942470295100
4.82-5.20.04539.422226271100
5.2-5.70.04836.472032252100
5.7-6.370.04835.91181622899.6
6.37-7.360.04143.141622204100
7.36-9.010.03346.881385186100
9.01-12.750.0353.35103414899.3
12.750.03245.84708584.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.1 Å
Translation3 Å44.1 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→44.14 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.2265 / WRfactor Rwork: 0.1812 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8377 / SU B: 22.597 / SU ML: 0.212 / SU R Cruickshank DPI: 0.5137 / SU Rfree: 0.3121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 286 4.7 %RANDOM
Rwork0.198 ---
obs0.2003 6131 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.42 Å2 / Biso mean: 58.9129 Å2 / Biso min: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0 Å2
2---1.1 Å20 Å2
3---2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.85→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 0 14 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191129
X-RAY DIFFRACTIONr_bond_other_d0.0010.021002
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9221538
X-RAY DIFFRACTIONr_angle_other_deg0.81432290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61523.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99415172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.099159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
X-RAY DIFFRACTIONr_mcbond_it2.7884.459545
X-RAY DIFFRACTIONr_mcbond_other2.7784.454544
X-RAY DIFFRACTIONr_mcangle_it4.3836.672680
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 31 -
Rwork0.271 417 -
all-448 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.2964 Å / Origin y: 46.394 Å / Origin z: 20.7892 Å
111213212223313233
T0.1577 Å2-0.0209 Å2-0.0486 Å2-0.0386 Å20.0007 Å2--0.0832 Å2
L1.8921 °2-0.278 °2-0.4595 °2-1.5407 °20.4404 °2--1.348 °2
S0.02 Å °0.0447 Å °-0.0234 Å °-0.1816 Å °0.0523 Å °-0.0559 Å °0.0258 Å °-0.0796 Å °-0.0723 Å °

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