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- PDB-4cog: Crystal structure of kynurenine formamidase from Burkholderia cen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cog | ||||||
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Title | Crystal structure of kynurenine formamidase from Burkholderia cenocepacia | ||||||
![]() | KYNURENINE FORMAMIDASE | ||||||
![]() | HYDROLASE / KYNURENINE FORMAMIDASE (KYNB) / EC 3.5.1.9 / AEROBIC TRYPTOPHAN DEGRADATION VIA ANTHRANILATE. | ||||||
Function / homology | ![]() arylformamidase / formamidase activity / arylformamidase activity / anthranilate metabolic process / tryptophan catabolic process to kynurenine / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Diaz-Saez, L. / Srikannathasan, V. / Zoltner, M. / Hunter, W.N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.5 KB | Display | ![]() |
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PDB format | ![]() | 164 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.1 KB | Display | ![]() |
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Full document | ![]() | 508.6 KB | Display | |
Data in XML | ![]() | 47 KB | Display | |
Data in CIF | ![]() | 69.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 22890.199 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 1106 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 14 % (W/V) PEG 3350, 5 MM COCL2, 5 MM CDCL2, 5 MM MGCL2 AND 5 MM NICL2. 293 K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28.37 Å / Num. obs: 134904 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: KYNURENINE FORMAMIDASE FROM PSEUDOMONAS AERUGINOSA Resolution: 1.6→134.84 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.414 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.074 / 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: 18.874 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→134.84 Å
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Refine LS restraints |
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