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Yorodumi- PDB-4e11: Crystal structure of kynurenine formamidase from Drosophila melan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 400000000000 | ||||||
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Title | Crystal structure of kynurenine formamidase from Drosophila melanogaster | ||||||
Components | kynurenine formamidase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold | ||||||
Function / homology | Function and homology information arylformamidase / arylformamidase activity / tryptophan catabolic process to kynurenine Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Han, Q. / Robinson, H. / Li, J. | ||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: Biochemical identification and crystal structure of kynurenine formamidase from Drosophila melanogaster. Authors: Han, Q. / Robinson, H. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e11.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e11.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 4e11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/4e11 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e11 | HTTPS FTP |
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-Related structure data
Related structure data | 4e14C 4e15C 2pblS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35217.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9542, Dmel_CG9542 / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VMC9, arylformamidase | ||||
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#2: Chemical | ChemComp-BME / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20558 / Num. obs: 19948 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.62 / Num. unique all: 1994 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PBL Resolution: 2→42.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.669 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.526 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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