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Yorodumi- PDB-2wwr: Crystal Structure of Human Glyoxylate Reductase Hydroxypyruvate R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wwr | ||||||
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Title | Crystal Structure of Human Glyoxylate Reductase Hydroxypyruvate Reductase | ||||||
Components | GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / MOLECULAR CONFORMATION | ||||||
Function / homology | Function and homology information dicarboxylic acid metabolic process / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / glyoxylate metabolic process / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process ...dicarboxylic acid metabolic process / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / glyoxylate metabolic process / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process / peroxisomal matrix / catalytic complex / NADPH binding / NAD binding / protein homodimerization activity / extracellular exosome / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | ||||||
Authors | Booth, M.P.S. / Conners, R. / Rumsby, G. / Brady, R.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Basis of Substrate Specificity in Human Glyoxylate Reductase/Hydroxypyruvate Reductase. Authors: Booth, M.P. / Conners, R. / Rumsby, G. / Brady, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wwr.cif.gz | 248.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwr.ent.gz | 200.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wwr_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 2wwr_full_validation.pdf.gz | 486.3 KB | Display | |
Data in XML | 2wwr_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 2wwr_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwr ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwr | HTTPS FTP |
-Related structure data
Related structure data | 2gcgSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper:
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-Components
#1: Protein | Mass: 35869.363 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRCHISB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9UBQ7, glyoxylate reductase (NADP+) #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | FIRST TWO RESIDUES IN CHAIN SEQUENCE ARE CLONING ARTIFACTS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.5 % / Description: NONE |
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Crystal grow | Details: 0.1M SODIUM CACODYLATE PH 6.75, 10% PEG 8K, 0.25M MAGNESIUM ACETATE TETRAHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.95 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 34609 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GCG Resolution: 2.82→100 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 31.778 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / 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: 36.093 Å2
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Refinement step | Cycle: LAST / Resolution: 2.82→100 Å
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Refine LS restraints |
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