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Yorodumi- PDB-4co9: Crystal structure of kynurenine formamidase from Bacillus anthracis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4co9 | ||||||
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Title | Crystal structure of kynurenine formamidase from Bacillus anthracis | ||||||
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 | BACILLUS ANTHRACIS (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 4co9.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4co9.ent.gz | 157.5 KB | Display | PDB format |
PDBx/mmJSON format | 4co9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4co9_validation.pdf.gz | 472.1 KB | Display | wwPDB validaton report |
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Full document | 4co9_full_validation.pdf.gz | 477 KB | Display | |
Data in XML | 4co9_validation.xml.gz | 41 KB | Display | |
Data in CIF | 4co9_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4co9 ftp://data.pdbj.org/pub/pdb/validation_reports/co/4co9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23414.561 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81PP9, arylformamidase |
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-Non-polymers , 5 types, 924 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: 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: 2.22 Å3/Da / Density % sol: 44.06 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 100 MM TRIS-HCL PH 8.5, 150 MM MGCL2, 30 % (W/V) PEG 4000 AND 1.5 % (V/V) DIOXANE. 293 K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Jul 27, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.48 Å / Num. obs: 202165 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.3 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: KYNURENINE FORMAMIDASE FROM BURKHOLDERIA CENOCEPACIA. TO BE SUBMITED Resolution: 1.95→83.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.595 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.152 / 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: 15.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→83.76 Å
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Refine LS restraints |
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