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Yorodumi- PDB-1j04: Structural mechanism of enzyme mistargeting in hereditary kidney ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j04 | ||||||
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Title | Structural mechanism of enzyme mistargeting in hereditary kidney stone disease in vitro | ||||||
Components | alanine--glyoxylate aminotransferase | ||||||
Keywords | TRANSFERASE / Aminotransferase / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / L-serine metabolic process ...oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / L-serine metabolic process / L-cysteine catabolic process / Glyoxylate metabolism and glycine degradation / amino acid binding / transaminase activity / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / peroxisome / protein self-association / pyridoxal phosphate binding / intracellular membrane-bounded organelle / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zhang, X. / Djordjevic, S. / Bartlam, M. / Ye, S. / Rao, Z. / Danpure, C.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structural implications of a G170R mutation of alanine:glyoxylate aminotransferase that is associated with peroxisome-to-mitochondrion mistargeting. Authors: Djordjevic, S. / Zhang, X. / Bartlam, M. / Ye, S. / Rao, Z. / Danpure, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j04.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j04.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j04 ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j04 | HTTPS FTP |
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-Related structure data
Related structure data | 1h0cS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43391.098 Da / Num. of mol.: 1 / Mutation: G170R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase | ||
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#2: Chemical | ChemComp-AOA / ( | ||
#3: Chemical | ChemComp-GOL / #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: 3.24 Å3/Da / Density % sol: 61.79 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2002 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 231743 / Num. obs: 18539 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.6→2.68 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1497 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H0C Resolution: 2.6→47.4 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.69 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→47.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Rfactor Rfree error: 0.021
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