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Yorodumi- PDB-4cob: Crystal structure kynurenine formamidase from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cob | ||||||
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Title | Crystal structure kynurenine formamidase from Pseudomonas aeruginosa | ||||||
Components | KYNURENINE FORMAMIDASE | ||||||
Keywords | HYDROLASE / AEROBIC TRYPTOPHAN DEGRADATION VIA ANTHRANILATE | ||||||
Function / homology | Function and homology information arylformamidase / formamidase activity / arylformamidase activity / anthranilate metabolic process / tryptophan catabolic process to kynurenine / zinc ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Diaz-Saez, L. / Srikannathasan, V. / Zoltner, M. / Hunter, W.N. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Structure of Bacterial Kynurenine Formamidase Reveals a Crowded Binuclear-Zinc Catalytic Site Primed to Generate a Potent Nucleophile. Authors: Diaz-Saez, L. / Srikannathasan, V. / Zoltner, M. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cob.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cob.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4cob ftp://data.pdbj.org/pub/pdb/validation_reports/co/4cob | HTTPS FTP |
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-Related structure data
Related structure data | 4co9C 4cogC 4cz1C 1r61S C: citing same article (ref.) 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: 23358.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9I234, arylformamidase #2: Chemical | ChemComp-ZN / #3: 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: 2.41 Å3/Da / Density % sol: 49.04 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 0.1 M HEPES PH 7.5, 20 % (W/V) PEG [POLY(ETHYLENE GLYCOL)] 4000, AND 10 % (V/V) 2-PROPANOL. 293 K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→28.9 Å / Num. obs: 27365 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.37→2.46 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R61 Resolution: 2.37→97.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.732 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.169 / 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: 50.986 Å2
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Refinement step | Cycle: LAST / Resolution: 2.37→97.62 Å
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Refine LS restraints |
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