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Yorodumi- PDB-2ztw: Structure of 3-isopropylmalate dehydrogenase in complex with the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ztw | ||||||
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Title | Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ | ||||||
Components | 3-isopropylmalate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 3-isopropylmalate dehydrogenase / IPMDH / decarboxylating dehydrogenase / Leucine biosynthesis / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis / Cytoplasm / Magnesium / Manganese / Metal-binding / NAD | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Nango, E. / Kumasaka, T. / Eguchi, T. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2009 Title: Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor Authors: Nango, E. / Yamamoto, T. / Kumasaka, T. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ztw.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ztw.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ztw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ztw_validation.pdf.gz | 750.3 KB | Display | wwPDB validaton report |
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Full document | 2ztw_full_validation.pdf.gz | 756 KB | Display | |
Data in XML | 2ztw_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2ztw_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/2ztw ftp://data.pdbj.org/pub/pdb/validation_reports/zt/2ztw | HTTPS FTP |
-Related structure data
Related structure data | 1hexS 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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-Components
#1: Protein | Mass: 36825.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: leuB, TTHA1230 / Plasmid: pHB2 / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-DEI / ( |
#4: Chemical | ChemComp-MG / |
#5: 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: 3.91 Å3/Da / Density % sol: 68.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 4M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→89.8 Å / Num. obs: 15425 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.121 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.79→2.9 Å / Rmerge(I) obs: 0.495 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HEX Resolution: 2.79→25.88 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.2 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.476 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.649 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→25.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.787→2.858 Å / Total num. of bins used: 20
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