+Open data
-Basic information
Entry | Database: PDB / ID: 1idm | ||||||
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Title | 3-ISOPROPYLMALATE DEHYDROGENASE, LOOP-DELETED CHIMERA | ||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / CHIMERA | ||||||
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 | Sakurai, M. / Ohzeki, M. / Moriyama, H. / Sato, M. / Tanaka, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Structure of a loop-deleted variant of 3-isopropylmalate dehydrogenase from Thermus thermophilus: an internal reprieve tolerance mechanism. Authors: Sakurai, M. / Ohzeki, M. / Miyazaki, K. / Moriyama, H. / Sato, M. / Tanaka, N. / 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 | 1idm.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1idm.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 1idm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idm ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idm | 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: CIS PROLINE - PRO 141 |
-Components
#1: Protein | Mass: 36471.656 Da / Num. of mol.: 1 / Mutation: LOOP-DELETED MUTANT, ARG 82 AND LYS 83 DELETED Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 Description: HYBRID BETWEEN THERMUS IPMDH (332 RESIDUES) AND YEAST IPMDH (11 RESIDUES) Production host: Escherichia coli (E. coli) / Strain (production host): JA221 References: UniProt: P00351, UniProt: Q5SIY4*PLUS, 3-isopropylmalate dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.03 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 7.6 / Details: Sakurai, M., (1992) J.Biochem., 112, 173. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 26, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 27190 / % possible obs: 76 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.038 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 9999 Å / Num. measured all: 44526 / Rmerge(I) obs: 0.0379 |
-Processing
Software |
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Refinement | Resolution: 2.2→5 Å / σ(F): 3
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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