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Yorodumi- PDB-4jbu: 1.65A structure of the T3SS tip protein LcrV (G28-D322, C273S) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jbu | ||||||
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Title | 1.65A structure of the T3SS tip protein LcrV (G28-D322, C273S) from Yersinia pestis | ||||||
Components | Virulence-associated V antigen | ||||||
Keywords | PROTEIN BINDING / LcrV / T3SS / tip protein / Yersinia pestis | ||||||
Function / homology | Low calcium response V antigen / Virulence-associated V antigen superfamily / V antigen (LcrV) protein / extracellular region / Virulence-associated V antigen Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Lovell, S. / Chaudhury, S. / Battaile, K.P. / Plano, G. / De Guzman, R.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of the Yersinia pestis tip protein LcrV refined to 1.65A resolution Authors: Chaudhury, S. / Battaile, K.P. / Lovell, S. / Plano, G.V. / De Guzman, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jbu.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jbu.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jbu_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 4jbu_full_validation.pdf.gz | 431.4 KB | Display | |
Data in XML | 4jbu_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4jbu_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/4jbu ftp://data.pdbj.org/pub/pdb/validation_reports/jb/4jbu | HTTPS FTP |
-Related structure data
Related structure data | 1r6fS S: Starting model for refinement |
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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: 33959.305 Da / Num. of mol.: 1 / Fragment: UNP residues 28-322 / Mutation: C273S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Plasmid: pGEV2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) DNAY / References: UniProt: P0C7U7 |
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#2: Chemical | ChemComp-PG4 / |
#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: 1.95 Å3/Da / Density % sol: 36.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 25% (w/v) PEG 3350, 100 mM Bicine, pH 7.0, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→51.44 Å / Num. all: 31392 / Num. obs: 31392 / % possible obs: 99.32 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.29 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 17.9825 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R6F Resolution: 1.65→34.33 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.24 / σ(F): 0 / Phase error: 20.77 / 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 / Bsol: 35.626 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.22 Å2 / Biso mean: 28.5916 Å2 / Biso min: 11.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→34.33 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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