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- PDB-4lso: Crystal structure of the soluble domain of a Type IV secretion sy... -

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Basic information

Entry
Database: PDB / ID: 4lso
TitleCrystal structure of the soluble domain of a Type IV secretion system protein VirB8 from Bartonella quintana Toulouse
ComponentsType IV secretion system protein virB8
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dimer-monomer analysis / type IV secretion system / innate response / human pathogen / host specific protein / cell adhesion
Function / homology
Function and homology information


protein secretion by the type IV secretion system / 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 speciesBartonella quintana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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
DepositionJul 22, 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 1.3Sep 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

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Assembly

Deposited unit
A: Type IV secretion system protein virB8


Theoretical massNumber of molelcules
Total (without water)20,8901
Polymers20,8901
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.730, 60.730, 87.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Type IV secretion system protein virB8


Mass: 20890.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: JK 31 / Gene: BQ10590, virB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FYW3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: BaquA.18388.b.B2.PS01732 at 21 mg/mL against JCSG+ screen condition B9, 0.1 M Na citrate pH 5.0, 20% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 242024b9, ...Details: BaquA.18388.b.B2.PS01732 at 21 mg/mL against JCSG+ screen condition B9, 0.1 M Na citrate pH 5.0, 20% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 242024b9, unique puck ID fez5-10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 18788 / Num. obs: 18752 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 34.27
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.740.4294.721100
1.74-1.790.3196.341100
1.79-1.840.2438.311100
1.84-1.90.1910.371100
1.9-1.960.14213.441100
1.96-2.030.10418.311100
2.03-2.110.08721.481100
2.11-2.190.0726.071100
2.19-2.290.05532.011100
2.29-2.40.04736.31100
2.4-2.530.04240.41100
2.53-2.690.03545.761100
2.69-2.870.03153.041100
2.87-3.10.02662.421100
3.1-3.40.02273.031100
3.4-3.80.02180.031100
3.8-4.390.01886.021100
4.39-5.380.01589.541100
5.38-7.60.01681.33199.8
7.60.01575.75187.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å43.93 Å
Translation3 Å43.93 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kz1

4kz1


Resolution: 1.7→43.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.333 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20713 960 5.1 %RANDOM
Rwork0.17415 ---
obs0.17581 17738 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 0 162 1282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191168
X-RAY DIFFRACTIONr_bond_other_d0.0010.021054
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9391594
X-RAY DIFFRACTIONr_angle_other_deg0.75532406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85223.50957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25415183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.886158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
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_it1.1881.649571
X-RAY DIFFRACTIONr_mcbond_other1.1711.646570
X-RAY DIFFRACTIONr_mcangle_it1.922.461714
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6021.78597
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.69232222
X-RAY DIFFRACTIONr_sphericity_free29.894541
X-RAY DIFFRACTIONr_sphericity_bonded7.92652314
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 85 -
Rwork0.203 1272 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -7.7746 Å / Origin y: 25.9968 Å / Origin z: -4.4987 Å
111213212223313233
T0.0228 Å20.0069 Å20.0018 Å2-0.0294 Å20.0092 Å2--0.0321 Å2
L1.4836 °2-0.0984 °2-0.4843 °2-1.2479 °2-0.3883 °2--1.5251 °2
S-0.0795 Å °-0.0835 Å °-0.1769 Å °-0.0063 Å °0.0235 Å °0.1124 Å °-0.0035 Å °-0.0334 Å °0.056 Å °

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