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- PDB-4kz1: Crystal structure of the soluble domain of VirB8 from Bartonella ... -

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Basic information

Entry
Database: PDB / ID: 4kz1
TitleCrystal structure of the soluble domain of VirB8 from Bartonella grahamii
ComponentsVirB8 protein
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / type IV secretion sequence / host-specific pathogen / Trw family / immune response / cell adhesion / weak dimer
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 grahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: VirB8 protein


Theoretical massNumber of molelcules
Total (without water)20,9311
Polymers20,9311
Non-polymers00
Water36020
1
A: VirB8 protein

A: VirB8 protein


Theoretical massNumber of molelcules
Total (without water)41,8632
Polymers41,8632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.620, 60.620, 124.570
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: 20931.441 Da / Num. of mol.: 1 / Fragment: soluble domain (UNP residues 51-222)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella grahamii (bacteria) / Strain: as4aup / Gene: Bgr_14870, virB8 / Production host: Escherichia coli (E. coli) / References: UniProt: C6AER9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BagrA.18388.a.B2.PW37031 at 6.35 mg/mL against MCSG1 screen condition E6, 0.2 M potassium sulfate, 20% PEG 3350 with 15% ethylene glycol as cryo-protectant; crystal tracking ID 238817e6, ...Details: BagrA.18388.a.B2.PW37031 at 6.35 mg/mL against MCSG1 screen condition E6, 0.2 M potassium sulfate, 20% PEG 3350 with 15% ethylene glycol as cryo-protectant; crystal tracking ID 238817e6, unique puck ID acy5-8, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 8095 / Num. obs: 8063 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 66.526 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 42.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.55-2.620.5063.82402457999.7
2.62-2.690.3864.913874562100
2.69-2.770.3076.263874560100
2.77-2.850.228.68361552499.8
2.85-2.940.15712.07359252699.8
2.94-3.050.11915.913430506100
3.05-3.160.08621.74330648499.8
3.16-3.290.05631.133199475100
3.29-3.440.04240.462995445100
3.44-3.610.03350.472942444100
3.61-3.80.02659.972728416100
3.8-4.030.02170.87249739599.7
4.03-4.310.01879.8235038099.7
4.31-4.660.01692.122177351100
4.66-5.10.01792.091958327100
5.1-5.70.01690.26176829499
5.7-6.580.01694.11733275100
6.58-8.060.014105.671422229100
8.06-11.40.011109.87107718997.9
11.40.01299.5446810285

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å41.52 Å
Translation3 Å41.52 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
Starting model: 4jf8

4jf8


Resolution: 2.55→35.34 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2369 / WRfactor Rwork: 0.1869 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8218 / SU B: 17.108 / SU ML: 0.176 / SU R Cruickshank DPI: 0.303 / SU Rfree: 0.2438 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 369 4.6 %RANDOM
Rwork0.203 ---
obs0.2051 8063 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.96 Å2 / Biso mean: 65.4664 Å2 / Biso min: 42.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-0 Å2
2---0.89 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.55→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 0 20 1096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191103
X-RAY DIFFRACTIONr_bond_other_d0.0010.02979
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.921502
X-RAY DIFFRACTIONr_angle_other_deg0.75832230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24623.62158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80815165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.424158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_mcbond_it2.7864.832539
X-RAY DIFFRACTIONr_mcbond_other2.7684.826538
X-RAY DIFFRACTIONr_mcangle_it4.2897.234672
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 31 -
Rwork0.337 548 -
all-579 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: -7.1933 Å / Origin y: 14.3623 Å / Origin z: 20.7116 Å
111213212223313233
T0.1887 Å20.0225 Å20.0331 Å2-0.0768 Å2-0.0258 Å2--0.1401 Å2
L0.6418 °2-0.0454 °20.0183 °2-1.864 °2-0.7635 °2--1.8256 °2
S0.0474 Å °-0.0605 Å °0.0583 Å °-0.2835 Å °0.0307 Å °0.0157 Å °0.0855 Å °0.2875 Å °-0.0781 Å °

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