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Yorodumi- PDB-2y3z: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y3z | ||||||
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Title | Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - apo enzyme | ||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / LEUB / LEUCINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / leucine biosynthetic process / NAD binding / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 | 2y3z.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y3z.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 2y3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/2y3z ftp://data.pdbj.org/pub/pdb/validation_reports/y3/2y3z | HTTPS FTP |
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-Related structure data
Related structure data | 2y40C 2y41C 2y42C 1hexS S: Starting model for refinement C: citing same article (ref.) |
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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: 38398.883 Da / Num. of mol.: 1 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 | ||||||
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#2: Chemical | ChemComp-TRS / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | POLYETHYLE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 35% PEG-550-MME, 0.1 M TRIS-HCL PH 9.0, 0.1 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→99 Å / Num. obs: 47324 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HEX Resolution: 1.83→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.53 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.093 / 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: 32.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→40 Å
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Refine LS restraints |
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