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Yorodumi- PDB-3efy: Structure of the Cyclomodulin Cif from Pathogenic Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 3efy | ||||||
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Title | Structure of the Cyclomodulin Cif from Pathogenic Escherichia coli | ||||||
Components | Cif (Cell cycle inhibiting factor) | ||||||
Keywords | CELL CYCLE / Cif / bacteria / virulence factor / type III secretion / E. coli / Plasmid | ||||||
Function / homology | Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / cell division / Cell cycle inhibiting factor Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Stebbins, C.E. / Hsu, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of the cyclomodulin Cif from pathogenic Escherichia coli. Authors: Hsu, Y. / Jubelin, G. / Taieb, F. / Nougayrede, J.P. / Oswald, E. / Stebbins, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3efy.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3efy.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 3efy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3efy ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3efy | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22440.434 Da / Num. of mol.: 2 / Fragment: UNP residues 100-282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cif / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WRZ5 #2: 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: 3.74 Å3/Da / Density % sol: 67.12 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 1.85M Sodium Malonate, 0.1M tri-sodium citrate dihydrate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 74589 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→45.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.555 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.088 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→45.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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