+Open data
-Basic information
Entry | Database: PDB / ID: 3ov5 | ||||||
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Title | Atomic structure of the Xanthomonas citri VirB7 globular domain. | ||||||
Components | Uncharacterized protein | ||||||
Keywords | PROTEIN TRANSPORT / Type IV secretion system component / VirB7 (XAC2622) / Bacterial outer membrane / XANTHOMONAS AXONOPODIS PV CITRI | ||||||
Function / homology | Phage 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 species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Souza, D.P. / Farah, C.S. | ||||||
Citation | Journal: 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 |
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Remark 999 | MET A 50 is INITIATING METHIONINE and CLONING ARTIFACT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ov5.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ov5.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ov5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/3ov5 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/3ov5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-IPA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 31.05 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 30, 2009 |
Radiation | Monochromator: Vertical collimator mirror + double Si(111) crystal monochromator + toroidal focus mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.366 Å2
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Refinement step | Cycle: LAST / Resolution: 1.04→23.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.04→1.067 Å / Total num. of bins used: 20
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