[English] 日本語
Yorodumi- PDB-1iyd: CRYSTAL STRUCTURE OF ESCHELICHIA COLI BRANCHED-CHAIN AMINO ACID A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iyd | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF ESCHELICHIA COLI BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE | ||||||
Components | BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE / HEXAMER / PLP | ||||||
Function / homology | Function and homology information aspartate biosynthetic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process ...aspartate biosynthetic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Hirotsu, K. / Goto, M. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal structures of branched-chain amino Acid aminotransferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme. Authors: Goto, M. / Miyahara, I. / Hayashi, H. / Kagamiyama, H. / Hirotsu, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1iyd.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1iyd.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 1iyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iyd_validation.pdf.gz | 414 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1iyd_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 1iyd_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 1iyd_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/1iyd ftp://data.pdbj.org/pub/pdb/validation_reports/iy/1iyd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34131.586 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pUC119 / Production host: Escherichia coli (E. coli) References: UniProt: P0AB80, branched-chain-amino-acid transaminase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, HEPES, MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→19.96 Å / Num. all: 58165 / Num. obs: 58165 / % possible obs: 99.5 % |
Reflection shell | Resolution: 2.15→2.22 Å / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 324820 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 96.8 % / Rmerge(I) obs: 0.195 |
-Processing
Software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→10 Å / σ(F): 2
| |||||||||||||||
Refine analyze |
| |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→10 Å
| |||||||||||||||
Refine LS restraints |
| |||||||||||||||
Refinement | *PLUS Lowest resolution: 19.96 Å | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.15 Å / Lowest resolution: 2.22 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.259 |