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Yorodumi- PDB-1dju: CRYSTAL STRUCTURE OF AROMATIC AMINOTRANSFERASE FROM PYROCOCCUS HO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dju | ||||||
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Title | CRYSTAL STRUCTURE OF AROMATIC AMINOTRANSFERASE FROM PYROCOCCUS HORIKOSHII OT3 | ||||||
Components | AROMATIC AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / ALPHA/BETA/ALPHA | ||||||
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 / Resolution: 2.1 Å | ||||||
Authors | Matsui, I. / Matsui, E. / Sakai, Y. / Kikuchi, H. / Kawarabayashi, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii. Authors: Matsui, I. / Matsui, E. / Sakai, Y. / Kikuchi, H. / Kawarabayasi, 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 | 1dju.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dju.ent.gz | 129.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dju_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 1dju_full_validation.pdf.gz | 481.2 KB | Display | |
Data in XML | 1dju_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 1dju_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/1dju ftp://data.pdbj.org/pub/pdb/validation_reports/dj/1dju | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43843.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Production host: Escherichia coli (E. coli) / References: UniProt: O59096 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.07 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1,6-HEXANE-DI-OL, MAGNESIUM CHLORIDE, PYRIDOXAL-5'-PHOSPHATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 10, 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: 2.1→28 Å / Num. all: 57422 / Num. obs: 57422 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.184 / % possible all: 70.1 |
Reflection | *PLUS Num. measured all: 359213 |
Reflection shell | *PLUS % possible obs: 70.1 % |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / σ(F): 2 / Stereochemistry target values: CHARMM BY BROOKS ET AL. / Details: ENERGY MINIMIZATION
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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