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Yorodumi- PDB-1ipd: THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-IS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ipd | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-ISOPROPYLMALATE DEHYDROGENASE OF THERMUS THERMOPHILUS AT 2.2 ANGSTROMS RESOLUTION | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Imada, K. / Sato, M. / Tanaka, N. / Katsube, Y. / Matsuura, Y. / Oshima, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 A resolution. Authors: Imada, K. / Sato, M. / Tanaka, N. / Katsube, Y. / Matsuura, Y. / 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. #2: Journal: J.Biochem.(Tokyo) / Year: 1988 Title: Crystallization and Preliminary X-Ray Data for 3-Isopropylmalate Dehydrogenase of Thermus Thermophilus Authors: Katsube, Y. / Tanaka, N. / Takenaka, A. / Yamada, T. / Oshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ipd.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ipd.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ipd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/1ipd ftp://data.pdbj.org/pub/pdb/validation_reports/ip/1ipd | HTTPS FTP |
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-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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Atom site foot note | 1: RESIDUE 143 IS A CIS PROLINE. | ||||||||
Details | THE FUNCTIONAL DIMER IN SOLUTION CAN BE GENERATED BY APPLYING THE SYMMETRY OPERATOR (-X, -X+Y, -Z-1/3) TO THE ATOMIC COORDINATED PRESENTED IN THIS ENTRY. |
-Components
#1: Protein | Mass: 36755.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE USED IS THAT PROVIDED BY THE AUTHORS (JRNL). | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.91 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting dropDetails: taken from Karsube, Y. et al (1988). J. Biochem., 104, 679-680. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 24478 / % possible obs: 83 % / Num. measured all: 42499 / Rmerge(I) obs: 0.0419 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→5 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 2.2→5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 5 Å / Num. reflection obs: 20307 / σ(F): 3 / Rfactor obs: 0.185 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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