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- PDB-4o3v: Crystal structure of a VirB8-like protein of type IV secretion sy... -

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Basic information

Entry
Database: PDB / ID: 4o3v
TitleCrystal structure of a VirB8-like protein of type IV secretion system from Rickettsia typhi
ComponentsVirB8-like protein of type IV secretion systemSecretion
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / secretion system / TrwG / murine / typhus / virulence / pathogenesis
Function / homology
Function and homology information


VirB8 protein / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / VirB8-like protein of type IV secretion system
Similarity search - Component
Biological speciesRickettsia typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: 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.
#1: Journal: Pathog Dis / Year: 2016
Title: The Rickettsia type IV secretion system: unrealized complexity mired by gene family expansion.
Authors: Gillespie, J.J. / Phan, I.Q. / Driscoll, T.P. / Guillotte, M.L. / Lehman, S.S. / Rennoll-Bankert, K.E. / Subramanian, S. / Beier-Sexton, M. / Myler, P.J. / Rahman, M.S. / Azad, A.F.
History
DepositionDec 18, 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 1.3Jun 29, 2016Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VirB8-like protein of type IV secretion system
B: VirB8-like protein of type IV secretion system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5693
Polymers42,4192
Non-polymers1501
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-7 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.680, 117.680, 83.820
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-like protein of type IV secretion system / Secretion


Mass: 21209.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia typhi (bacteria) / Strain: VR-144 / Willmington / Gene: RT0278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68X84
#2: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: RityA.18390.a.B2 PS01633 at 11.2 mg/mL against CSHT A2, 0.4 M potassium sodium tartrate, cryo-protected with Al's oil, crystal grew over 7 months, crystal tracking ID 250519a2, unique puck ...Details: RityA.18390.a.B2 PS01633 at 11.2 mg/mL against CSHT A2, 0.4 M potassium sodium tartrate, cryo-protected with Al's oil, crystal grew over 7 months, crystal tracking ID 250519a2, unique puck ID zuk7-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 43393 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 30.753 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.4774.15292493147100
2-2.060.3665.61301673075100
2.06-2.120.2897.2329281299699.9
2.12-2.180.2349.01286922921100
2.18-2.250.20410.56277162830100
2.25-2.330.17512.32266972748100
2.33-2.420.14214.85258522637100
2.42-2.520.12716.65247602544100
2.52-2.630.11518.78241062467100
2.63-2.760.08923.44227172326100
2.76-2.910.07627.41218172244100
2.91-3.080.05834.96206152134100
3.08-3.30.04841.5190522001100
3.3-3.560.04247.42175831871100
3.56-3.90.03552.99161831737100
3.9-4.360.03257.06145491584100
4.36-5.030.02959.7312710140199.9
5.03-6.170.03153.93108271206100
6.17-8.720.02756.448683954100
8.720.02262.17465957098.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1783 / WRfactor Rwork: 0.1581 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8921 / SU B: 3.819 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0961 / SU Rfree: 0.0948 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 2182 5 %RANDOM
Rwork0.1656 ---
obs0.1667 43389 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.88 Å2 / Biso mean: 31.9189 Å2 / Biso min: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0 Å20 Å2
2---1.07 Å2-0 Å2
3---2.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 10 318 2554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022363
X-RAY DIFFRACTIONr_bond_other_d0.0010.022228
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9393222
X-RAY DIFFRACTIONr_angle_other_deg0.80535098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05225.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74515419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7041511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_mcbond_it2.0092.2061138
X-RAY DIFFRACTIONr_mcbond_other2.0062.2021137
X-RAY DIFFRACTIONr_mcangle_it3.163.2721423
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 150 -
Rwork0.199 2991 -
all-3141 -
obs--100 %
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)
12.48060.4288-0.70771.210.00550.6988-0.0311-0.1208-0.19530.10060.0169-0.15720.05360.06320.01420.01630.0136-0.02030.0248-0.01940.06427.463463.046624.8894
21.9004-0.4073-0.21081.25570.32540.85140.0038-0.0220.1-0.12220.048-0.1492-0.08140.0904-0.05180.0429-0.02460.01950.0296-0.02840.049826.93254.09844.3365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A90 - 231
2X-RAY DIFFRACTION2B90 - 231

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