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Yorodumi- PDB-2y42: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -
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-Basic information
Entry | Database: PDB / ID: 2y42 | ||||||
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Title | Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH and Mn | ||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / LEUB / LEUCINE BIOSYNTHESIS | ||||||
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: 2.5 Å | ||||||
Authors | Graczer, E. / merlin, A. / Singh, R.K. / Manikandan, K. / Zavodsky, P. / Weiss, M.S. / Vas, M. | ||||||
Citation | Journal: Mol.Biosyst. / Year: 2011 Title: Atomic Level Description of the Domain Closure in a Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase. Authors: Graczer, E. / Merli, A. / Singh, R.K. / Karuppasamy, M. / Zavodszky, P. / Weiss, M.S. / Vas, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Various Enzyme-Substrate Complexes of Isopropylmalate Dehydrogenase from Thermus Thermophilus. Authors: Merli, A. / Manikandan, K. / Graczer, E. / Schuldt, L. / Singh, R.K. / Zavodszky, P. / Vas, M. / Weiss, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y42.cif.gz | 538.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y42.ent.gz | 446.4 KB | Display | PDB format |
PDBx/mmJSON format | 2y42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y42_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2y42_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2y42_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 2y42_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y42 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y42 | HTTPS FTP |
-Related structure data
Related structure data | 2y3zSC 2y40C 2y41C C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38398.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: ADDITIONAL AMINO ACIDS- N-TERMINAL MAS.C- TERMINAL AAALEHHHHHH Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase #2: Chemical | ChemComp-BCN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-MN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 15% PEG-20000, 2% DIOXANE, 0.1 M BICINE PH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. obs: 51742 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y3Z Resolution: 2.5→19.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.89 / SU B: 22.297 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.304 / 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: 49.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.72 Å
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