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Yorodumi- PDB-1xaa: 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xaa | ||||||
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Title | 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE | ||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Nagata, C. / Moriyama, H. / Tanaka, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Cryocrystallography of 3-Isopropylmalate dehydrogenase from Thermus thermophilus and its chimeric enzyme. Authors: Nagata, C. / Moriyama, H. / Tanaka, N. / Nakasako, M. / Yamamoto, M. / Ueki, T. / Oshima, T. #1: Journal: J.Biochem.(Tokyo) / Year: 1990 Title: Purification, Catalytic Properties and Thermal Stability of Threo-Ds-3-Isopropylmalate Dehydrogenase Coded by Leub Gene from an Extreme Thermophile, Thermus Thermophilus Strain Hb8 Authors: Yamada, T. / Akutsu, N. / Miyazaki, K. / Kakinuma, K. / Yoshida, M. / Oshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xaa.cif.gz | 104.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xaa.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xaa_validation.pdf.gz | 364.7 KB | Display | wwPDB validaton report |
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Full document | 1xaa_full_validation.pdf.gz | 371.5 KB | Display | |
Data in XML | 1xaa_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1xaa_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/1xaa ftp://data.pdbj.org/pub/pdb/validation_reports/xa/1xaa | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 143 |
-Components
#1: Protein | Mass: 36825.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: LOW TEMPERATURE (100K) STRUCTURE / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.13 % | ||||||||||||||||||||
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Crystal | *PLUS Density % sol: 67.3 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 100 K / pH: 7.5 / Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 8, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 19388 / % possible obs: 59.8 % / Observed criterion σ(I): 1 / Redundancy: 0.598 % / Rmerge(I) obs: 0.058 |
Reflection | *PLUS Highest resolution: 2.1 Å / Rmerge(I) obs: 0.058 |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.99 |