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Yorodumi- PDB-1gck: THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE DOUBLE MUTANT 1 C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gck | ||||||
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Title | THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE DOUBLE MUTANT 1 COMPLEXED WITH ASPARTATE | ||||||
Components | ASPARTATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / Aminotransferase / Dual-substrate enzyme / Pyridoxal enzyme | ||||||
Function / homology | Function and homology information aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Ura, H. / Nakai, T. / Hirotsu, K. / Kuramitsu, S. | ||||||
Citation | Journal: J.Biochem. / Year: 2001 Title: Substrate recognition mechanism of thermophilic dual-substrate enzyme. Authors: Ura, H. / Nakai, T. / Kawaguchi, S.I. / Miyahara, I. / Hirotsu, K. / Kuramitsu, S. #1: Journal: Biochemistry / Year: 1999 Title: Structure of Thermus thermophilus HB8 Aspartate Aminotransferase and its Complex with Maleate. Authors: Nakai, T. / Okada, K. / Akutsu, S. / Miyahara, I. / Kawaguchi, S. / Kato, R. / Kuramitsu, S. / Hirotsu, K. #2: Journal: J.Biol.Chem. / Year: 1998 Title: The novel Substrate Recognition Mechanism Utilized by Aspartate Aminotransferase of the Extreme Thermophile thermus thermophilus HB8. Authors: Nobe, Y. / Kawaguchi, S. / Ura, H. / Nakai, T. / Hirotsu, K. / Kato, R. / Kuramitsu, S. #3: Journal: J.BIOCHEM.(TOKYO) / Year: 1996 Title: An Aspartate Aminotransferase from an Extremely Thermophilic Bacterium, Thermus thermophilus HB8. Authors: Okamoto, A. / Kato, R. / Masui, R. / Yamagishi, A. / Oshima, T. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gck.cif.gz | 157.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gck.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 1gck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gck_validation.pdf.gz | 479.1 KB | Display | wwPDB validaton report |
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Full document | 1gck_full_validation.pdf.gz | 501 KB | Display | |
Data in XML | 1gck_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 1gck_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gck ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gck | HTTPS FTP |
-Related structure data
Related structure data | 1b5oC 1b5pC 1gc3C 1gc4C 5bj3C 5bj4C C: citing same article (ref.) |
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Similar 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: 42130.949 Da / Num. of mol.: 2 / Mutation: K101S, S261R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q56232, aspartate transaminase #2: Chemical | #3: Chemical | #4: 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: 2.28 Å3/Da / Density % sol: 46.14 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 82422 / Num. obs: 24644 / % possible obs: 89.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 43.377 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.218 / % possible all: 88.7 |
Reflection | *PLUS Num. measured all: 82422 |
-Processing
Software |
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Refinement | Resolution: 2.5→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2 |