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Yorodumi- PDB-5evg: Crystal structure of a Francisella virulence factor FvfA in the o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5evg | ||||||||||||
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Title | Crystal structure of a Francisella virulence factor FvfA in the orthorhombic form | ||||||||||||
Components | Francisella virulence factor | ||||||||||||
Keywords | UNKNOWN FUNCTION / Francisella tularensis / virulence factor | ||||||||||||
Function / homology | membrane / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||||||||
Biological species | Francisella novicida (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||||||||
Authors | Kolappan, S. / Lo, K.Y. / Shen, C.L.J. / Guttman, J.A. / Craig, L. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Structure of the conserved Francisella virulence protein FvfA. Authors: Kolappan, S. / Lo, K.Y. / Shen, C.L.J. / Guttman, J.A. / Craig, L. #1: Journal: Infect. Immun. / Year: 2015 Title: Identifying Francisella tularensis genes required for growth in host cells. Authors: Brunton, J. / Steele, S. / Miller, C. / Lovullo, E. / Taft-Benz, S. / Kawula, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5evg.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5evg.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 5evg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5evg_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 5evg_full_validation.pdf.gz | 417.9 KB | Display | |
Data in XML | 5evg_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 5evg_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/5evg ftp://data.pdbj.org/pub/pdb/validation_reports/ev/5evg | HTTPS FTP |
-Related structure data
Related structure data | 5evfSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11902.308 Da / Num. of mol.: 1 / Fragment: UNP residues 32-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella novicida (bacteria) / Gene: ACX55_1794 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K1NSD0, UniProt: A0Q625*PLUS |
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#2: 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: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: Citric acid, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9753 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→37.4 Å / Num. obs: 10549 / % possible obs: 99.98 % / Redundancy: 7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.82→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EVF Resolution: 1.82→37.377 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→37.377 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.0868 Å / Origin y: -3.7139 Å / Origin z: -3.9024 Å
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Refinement TLS group | Selection details: all |