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Yorodumi- PDB-2rdt: Crystal Structure of Human Glycolate Oxidase (GO) in Complex with CDST -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rdt | ||||||
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Title | Crystal Structure of Human Glycolate Oxidase (GO) in Complex with CDST | ||||||
Components | Hydroxyacid oxidase 1 | ||||||
Keywords | OXIDOREDUCTASE / Flavoprotein / FMN / Glycolate pathway / Peroxisome | ||||||
Function / homology | Function and homology information glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / fatty acid alpha-oxidation / (S)-2-hydroxy-acid oxidase activity / Glyoxylate metabolism and glycine degradation / glycine biosynthetic process / peroxisomal matrix / Peroxisomal protein import ...glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / fatty acid alpha-oxidation / (S)-2-hydroxy-acid oxidase activity / Glyoxylate metabolism and glycine degradation / glycine biosynthetic process / peroxisomal matrix / Peroxisomal protein import / peroxisome / FMN binding / response to oxidative stress / intracellular membrane-bounded organelle / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Murray, M.S. / Holmes, R.P. / Lowther, W.T. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Active Site and Loop 4 Movements within Human Glycolate Oxidase: Implications for Substrate Specificity and Drug Design. Authors: Murray, M.S. / Holmes, R.P. / Lowther, W.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rdt.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rdt.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 2rdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/2rdt ftp://data.pdbj.org/pub/pdb/validation_reports/rd/2rdt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42640.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HAO1, GOX1, HAOX1 / Plasmid: pET28a / Cell line (production host): C41(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-2RD / |
#4: 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: 2.15 Å3/Da / Density % sol: 42.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: HEPES,PEG 600, CDST, pH 7.5, temperature 298K, pH 7.50, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 8, 2007 |
Radiation | 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→48.16 Å / Num. obs: 25585 / % possible obs: 96.8 % |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Resolution: 1.95→48.16 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.729 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å
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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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