+Open data
-Basic information
Entry | Database: PDB / ID: 1gd9 | ||||||
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Title | CRYSTALL STRUCTURE OF PYROCOCCUS PROTEIN-A1 | ||||||
Components | ASPARTATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / aminotransferase / pyridoxal enzyme / temperature dependence of substrate recognition | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Ura, H. / Harata, K. / Matsui, I. / Kuramitsu, S. | ||||||
Citation | Journal: J.Biochem. / Year: 2001 Title: Temperature dependence of the enzyme-substrate recognition mechanism. Authors: Ura, H. / Harata, K. / Matsui, I. / Kuramitsu, S. #1: Journal: J.Biol.Chem. / Year: 2000 Title: The Molecular Structure of Hypoerthermostable Aromatic Aminotransferase with Novel Substrate Specificity from Pyrococcus horikoshii Authors: Matsui, I. / Matsui, E. / Sakai, Y. / KIkuchi, H. / Kawarabayashi, Y. / Ura, H. / Kawaguchi, S. / Kuramitsu, S. / Harata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gd9.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gd9.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gd9_validation.pdf.gz | 460.1 KB | Display | wwPDB validaton report |
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Full document | 1gd9_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 1gd9_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 1gd9_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/1gd9 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/1gd9 | HTTPS FTP |
-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: 43960.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) References: UniProt: O59096, Transferases; Transferring nitrogenous groups; Transaminases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1,6-hexane diol, Tris, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: ADSC QUAMTUM 4r / Detector: CCD / Date: Jun 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 272833 / Num. obs: 83030 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.297 / Num. unique all: 11472 / % possible all: 96 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 272833 |
-Processing
Software |
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Refinement | Resolution: 1.8→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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