[English] 日本語
Yorodumi- PDB-1c9c: ASPARTATE AMINOTRANSFERASE COMPLEXED WITH C3-PYRIDOXAL-5'-PHOSPHATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c9c | ||||||
---|---|---|---|---|---|---|---|
Title | ASPARTATE AMINOTRANSFERASE COMPLEXED WITH C3-PYRIDOXAL-5'-PHOSPHATE | ||||||
Components | ASPARTATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / ENZYME-SUBSTRATE COMPLEX | ||||||
Function / homology | Function and homology information L-phenylalanine biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / aspartate catabolic 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1c9c.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1c9c.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c9c_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1c9c_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 1c9c_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1c9c_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9c ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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 |
---|---|
#2: Chemical | ChemComp-PP3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.69 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, potassium phosphate, C3-pyridoxal-5p-phosphate, sodium azide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 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. all: 104038 / Num. obs: 19863 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.22 / Num. unique all: 1947 / % possible all: 90.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 77327 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
| ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor obs: 0.202 / Rfactor Rfree: 0.271 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |