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- PDB-3ov5: Atomic structure of the Xanthomonas citri VirB7 globular domain. -

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Basic information

Entry
Database: PDB / ID: 3ov5
TitleAtomic structure of the Xanthomonas citri VirB7 globular domain.
ComponentsUncharacterized protein
KeywordsPROTEIN TRANSPORT / Type IV secretion system component / VirB7 (XAC2622) / Bacterial outer membrane / XANTHOMONAS AXONOPODIS PV CITRI
Function / homologyPhage tail protein beta-alpha-beta fold - #70 / Toxin co-regulated pilus biosynthesis protein Q, C-terminal / Toxin co-regulated pilus biosynthesis protein Q / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / Toxin co-regulated pilus biosynthesis protein Q C-terminal domain-containing protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsSouza, D.P. / Farah, C.S.
CitationJournal: Plos Pathog. / Year: 2011
Title: A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins.
Authors: Souza, D.P. / Andrade, M.O. / Alvarez-Martinez, C.E. / Arantes, G.M. / Farah, C.S. / Salinas, R.K.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999MET A 50 is INITIATING METHIONINE and CLONING ARTIFACT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0812
Polymers9,0211
Non-polymers601
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.760, 55.810, 83.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-183-

HOH

21A-192-

HOH

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Components

#1: Protein Uncharacterized protein / VirB7 (XAC2622)


Mass: 9021.133 Da / Num. of mol.: 1 / Fragment: Globular Domain, residues 51-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: XAC2622 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: Q8PJB3
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.78 Å3/Da / Density % sol: 31.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 14 mg/mL protein in 5 mM Tris-Cl pH 7.5 and 25 mM sodium chloride was submitted to vapor diffusion sitting-drop crystallization trials at 291 K. Large plates appeared after one day over a ...Details: 14 mg/mL protein in 5 mM Tris-Cl pH 7.5 and 25 mM sodium chloride was submitted to vapor diffusion sitting-drop crystallization trials at 291 K. Large plates appeared after one day over a reservoir solution comprising 1.4 M ammonium sulphate and 4 % (v/v) isopropyl alcohol. Reservoir solution supplemented with 25 % (v/v) glycerol was used as cryoprotectant. , VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 30, 2009
RadiationMonochromator: Vertical collimator mirror + double Si(111) crystal monochromator + toroidal focus mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.04→30 Å / Num. all: 30386 / Num. obs: 30320 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 5.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 34.8
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2449 / % possible all: 79

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Globular domain from NMR structure of the same protein.

Resolution: 1.04→23.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.674 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15161 1524 5 %RANDOM
Rwork0.13014 ---
all0.1312 28796 --
obs0.1312 28796 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.366 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---1.21 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.04→23.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 4 115 738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.691.971990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8826.66724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47615114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.847151
X-RAY DIFFRACTIONr_chiral_restr0.1060.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02539
X-RAY DIFFRACTIONr_nbd_refined0.2240.2333
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.223
X-RAY DIFFRACTIONr_mcbond_it1.5461.5481
X-RAY DIFFRACTIONr_mcangle_it2.22777
X-RAY DIFFRACTIONr_scbond_it2.6753263
X-RAY DIFFRACTIONr_scangle_it3.2814.5204
X-RAY DIFFRACTIONr_rigid_bond_restr1.3413744
X-RAY DIFFRACTIONr_sphericity_free7.8933117
X-RAY DIFFRACTIONr_sphericity_bonded6.8753691
LS refinement shellResolution: 1.04→1.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 84 -
Rwork0.191 1670 -
obs-1754 76.36 %

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