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Yorodumi- PDB-4oko: Crystal structure of Francisella tularensis REP34 (Rapid Encystme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oko | ||||||
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Title | Crystal structure of Francisella tularensis REP34 (Rapid Encystment Phenotype Protein 34 KDa) | ||||||
Components | Rapid Encystment Phenotype Protein 34 KDa | ||||||
Keywords | HYDROLASE / carboxypeptidase / secreted | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Francisella tularensis subsp. novicida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å | ||||||
Authors | Feld, G.K. / Segelke, B.W. / Corzett, M.H. / Hunter, M.S. / Frank, M. / Rasley, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structure and Function of REP34 Implicates Carboxypeptidase Activity in Francisella tularensis Host Cell Invasion. Authors: Feld, G.K. / El-Etr, S. / Corzett, M.H. / Hunter, M.S. / Belhocine, K. / Monack, D.M. / Frank, M. / Segelke, B.W. / Rasley, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oko.cif.gz | 427.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oko.ent.gz | 358 KB | Display | PDB format |
PDBx/mmJSON format | 4oko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/4oko ftp://data.pdbj.org/pub/pdb/validation_reports/ok/4oko | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35381.641 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. novicida (bacteria) Strain: U112 / Gene: FTN_0149 / Plasmid: pETBlue X1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0Q494, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% w/v PEG4000, 0.1 M sodium acetate, pH 4.7-5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.2837 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2012 / Details: minibeam 20x20x20 um |
Radiation | Monochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2837 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→22 Å / Num. all: 68959 / Num. obs: 68959 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 35.93 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 8.98 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.07 / Rsym value: 0.579 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAD SE-MET SOLUTION FOR ZN-FREE CRYSTAL Resolution: 2.053→21.535 Å / SU ML: 0.25 / σ(F): 1.98 / Phase error: 24.96 / 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: 2.053→21.535 Å
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Refine LS restraints |
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LS refinement shell |
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