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Yorodumi- PDB-1cq7: ASPARTATE AMINOTRANSFERASE (E.C. 2.6.1.1) COMPLEXED WITH C5-PYRID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cq7 | ||||||
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Title | ASPARTATE AMINOTRANSFERASE (E.C. 2.6.1.1) COMPLEXED WITH C5-PYRIDOXAL-5P-PHOSPHATE | ||||||
Components | ASPARTATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / ENZYME-SUBSTRATE COMPLEX | ||||||
Function / homology | Function and homology information L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Ishijima, J. / Nakai, T. / Kawaguchi, S. / Hirotsu, K. / Kuramitsu, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Free energy requirement for domain movement of an enzyme Authors: Ishijima, J. / Nakai, T. / Kawaguchi, S. / Hirotsu, K. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cq7.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cq7.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 1cq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cq7_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 1cq7_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 1cq7_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1cq7_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cq7 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cq7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE FUNCTIONAL DIMER CAN BE GENERATED BY APPLYING THE SYMMETRY OPERATOR (X, -Y, -Z) TO THE ATOMIC COORDINATES PRESENTED IN THIS ENTRY. |
-Components
#1: Protein | Mass: 43619.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase |
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#2: Chemical | ChemComp-PY5 / |
#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: 3.05 Å3/Da / Density % sol: 59.66 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, potassium phosphate, C4-pyridoxal-5p-phosphate,sodium azide , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 20972 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.317 / % possible all: 97.1 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 91223 |
-Processing
Software |
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Refinement | Resolution: 2.4→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.215 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |