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Yorodumi- PDB-1a05: CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a05 | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE | ||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DECARBOXYLATING DEHYDROGENASE / LEUCINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Acidithiobacillus ferrooxidans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Imada, K. / Inagaki, K. / Matsunami, H. / Kawaguchi, H. / Tanaka, H. / Tanaka, N. / Namba, K. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism. Authors: Imada, K. / Inagaki, K. / Matsunami, H. / Kawaguchi, H. / Tanaka, H. / Tanaka, N. / Namba, K. #1: Journal: Biosci.Biotechnol.Biochem. / Year: 1998 Title: Overproduction and Substrate Specificity of 3-Isopropylmalate Dehydrogenase from Thiobacillus Ferrooxidans Authors: Matsunami, H. / Kawaguchi, H. / Inagaki, K. / Eguchi, T. / Kakinuma, K. / Tanaka, H. #2: Journal: J.Biochem.(Tokyo) / Year: 1993 Title: 3-Isopropylmalate Dehydrogenase from Chemolithoautotroph Thiobacillus Ferrooxidans: DNA Sequence, Enzyme Purification, and Characterization Authors: Kawaguchi, H. / Inagaki, K. / Kuwata, Y. / Tanaka, H. / Tano, T. #3: Journal: J.Ferment.Bioeng. / Year: 1990 Title: Cloning and Expression of the Thiobacillus Ferrooxidans 3-Isopropylmalate Dehydrogenase Gene in Escherichia Coli Authors: Inagaki, K. / Kawaguchi, H. / Kuwata, Y. / Sugio, T. / Tanaka, H. / Tano, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a05.cif.gz | 156.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a05.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a05_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 1a05_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 1a05_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 1a05_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a05 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a05 | HTTPS FTP |
-Related structure data
Related structure data | 1ipdS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.00211, 0.00044), Vector: |
-Components
#1: Protein | Mass: 38505.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria) Strain: AP19-3 / Gene: LEUB / Plasmid: PKKLEUB1 / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 References: UniProt: Q56268, 3-isopropylmalate dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. obs: 44212 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.25 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 3.5 / % possible all: 86 |
Reflection shell | *PLUS % possible obs: 86 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IPD Resolution: 2→8 Å / Data cutoff high absF: 550 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 20.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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