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Yorodumi- PDB-3s5o: Crystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase Boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s5o | ||||||
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Title | Crystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase Bound to Pyruvate | ||||||
Components | 4-hydroxy-2-oxoglutarate aldolase, mitochondrial | ||||||
Keywords | LYASE / aldolase / beta barrel / Schiff base / hydroxyproline metabolism | ||||||
Function / homology | Function and homology information 4-hydroxyproline catabolic process / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 4-hydroxy-2-oxoglutarate aldolase activity / oxalate metabolic process / glyoxylate metabolic process / N-acetylneuraminate lyase activity / pyruvate biosynthetic process / glyoxylate catabolic process / N-acetylneuraminate catabolic process ...4-hydroxyproline catabolic process / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 4-hydroxy-2-oxoglutarate aldolase activity / oxalate metabolic process / glyoxylate metabolic process / N-acetylneuraminate lyase activity / pyruvate biosynthetic process / glyoxylate catabolic process / N-acetylneuraminate catabolic process / Glyoxylate metabolism and glycine degradation / mitochondrial matrix / protein homodimerization activity / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SAD / molecular replacement / Resolution: 1.97 Å | ||||||
Authors | Riedel, T.J. / Lowther, W.T. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Structural and Biochemical Studies of Human 4-hydroxy-2-oxoglutarate Aldolase: Implications for Hydroxyproline Metabolism in Primary Hyperoxaluria. Authors: Riedel, T.J. / Johnson, L.C. / Knight, J. / Hantgan, R.R. / 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 | 3s5o.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s5o.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/3s5o ftp://data.pdbj.org/pub/pdb/validation_reports/s5/3s5o | 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: 32979.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C10orf65, DHDPSL, HOGA1 / Plasmid: pMal / Production host: Escherichia coli (E. coli) References: UniProt: Q86XE5, 4-hydroxy-2-oxoglutarate aldolase | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-K / | #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: 4.75 Å3/Da / Density % sol: 74.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, KSCN, Bis tris Propane, TCEP, Ethelyene glycol, pH 7.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 29, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→35.17 Å / Num. obs: 45370 / % possible obs: 99.9 % / Redundancy: 13.82 % / Rmerge(I) obs: 0.05 / Χ2: 0.91 / Net I/σ(I): 20.8 / Scaling rejects: 4740 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.97→34.648 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.33 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.108 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.92 Å2 / Biso mean: 29.8862 Å2 / Biso min: 18.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→34.648 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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