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Yorodumi- PDB-1w7m: Crystal structure of human kynurenine aminotransferase I in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w7m | ||||||
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Title | Crystal structure of human kynurenine aminotransferase I in complex with L-Phe | ||||||
Components | KYNURENINE--OXOGLUTARATE TRANSAMINASE I | ||||||
Keywords | TRANSFERASE / KYNURENINE PATHWAY / KYNURENIC ACID / PLP-ENZYME / AMINOTRANSFERASE / LYASE / MULTIFUNCTIONAL ENZYME / PYRIDOXAL PHOSPHATE | ||||||
Function / homology | Function and homology information glutamine-phenylpyruvate transaminase / glutamine-phenylpyruvate transaminase activity / cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / cysteine-S-conjugate beta-lyase / Phenylalanine metabolism / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / Glutamate and glutamine metabolism ...glutamine-phenylpyruvate transaminase / glutamine-phenylpyruvate transaminase activity / cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / cysteine-S-conjugate beta-lyase / Phenylalanine metabolism / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / Glutamate and glutamine metabolism / Tryptophan catabolism / biosynthetic process / response to bacterium / pyridoxal phosphate binding / protein homodimerization activity / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Rossi, F. / Han, Q. / Li, J. / Li, J. / Rizzi, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structure of Human Kynurenine Aminotransferase I Authors: Rossi, F. / Han, Q. / Li, J. / Li, J. / Rizzi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w7m.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w7m.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 1w7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/1w7m ftp://data.pdbj.org/pub/pdb/validation_reports/w7/1w7m | HTTPS FTP |
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-Related structure data
Related structure data | 1w7lSC 1w7nC S: Starting model for refinement C: citing same article (ref.) |
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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: 47927.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q16773, cysteine-S-conjugate beta-lyase |
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#2: Chemical | ChemComp-PHE / |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
Compound details | CATALYTIC ACTIVITY: L-KYNURENINE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.24 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MSC / Detector: AREA DETECTOR / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 22371 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. measured all: 81664 / Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W7L Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.824 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.258 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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