+Open data
-Basic information
Entry | Database: PDB / ID: 2hzp | ||||||
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Title | Crystal Structure of Homo Sapiens Kynureninase | ||||||
Components | Kynureninase | ||||||
Keywords | HYDROLASE / kynureninase / kynurenine / hydroxykynurenine / PLP / pyridoxal phosphate / quinolinic acid / hydroxyanthranilate / 3-hydroxyanthranilate / vitamin B6 / NAD / quinolinate | ||||||
Function / homology | Function and homology information 3-hydroxykynureninase activity / kynureninase / kynureninase activity / response to vitamin B6 / L-kynurenine catabolic process / quinolinate biosynthetic process / anthranilate metabolic process / tryptophan catabolic process to kynurenine / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process ...3-hydroxykynureninase activity / kynureninase / kynureninase activity / response to vitamin B6 / L-kynurenine catabolic process / quinolinate biosynthetic process / anthranilate metabolic process / tryptophan catabolic process to kynurenine / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / NAD biosynthetic process / response to type II interferon / pyridoxal phosphate binding / protein homodimerization activity / mitochondrion / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lima, S. / Khristoforov, R. / Momany, C. / Phillips, R.S. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structure of Homo sapiens Kynureninase. Authors: Lima, S. / Khristoforov, R. / Momany, C. / Phillips, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hzp.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hzp.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/2hzp ftp://data.pdbj.org/pub/pdb/validation_reports/hz/2hzp | HTTPS FTP |
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-Related structure data
Related structure data | 1qz9S 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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Details | The biological assembly is a dimer that can be generated by applying the crystallographic symmetry operator -X, Y, -Z to the monomer. |
-Components
#1: Protein | Mass: 56575.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KYNU / Plasmid: pCRT7OHKYN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16719, kynureninase |
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#2: Chemical | ChemComp-PLP / |
#3: 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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 8 Details: A 9.2 mg/ml kynureninase solution in 50 mM HEPES pH 5.2, 0.2 mM PLP was mixed in equal parts with 0.1 M Tris-Cl pH 8.0, 0.05 M MgCl2, 25% PEG 3000, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2→88.39 Å / Num. obs: 33266 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.969 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 24.68 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 5.046 / Num. unique all: 3279 / Rsym value: 0.264 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QZ9 Resolution: 2→88.39 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.997 / SU ML: 0.091 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.144 / Stereochemistry target values: Engh & Huber
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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: 21.969 Å2
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Refinement step | Cycle: LAST / Resolution: 2→88.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.055 Å / Total num. of bins used: 20
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