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Yorodumi- PDB-4f7i: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f7i | ||||||
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Title | Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH | ||||||
Components | 3-isopropylmalate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ISOPROPYLMALATE DEHYDROGENASE / 3-IPM-DH / BETA-IPM DEHYDROGENASE / IMDH / IPMDH | ||||||
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 Å | ||||||
Authors | Pallo, A. / Graczer, E. / Zavodszky, P. / Weiss, M.S. / Vas, M. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis. Authors: Pallo, A. / Olah, J. / Graczer, E. / Merli, A. / Zavodszky, P. / Weiss, M.S. / Vas, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f7i.cif.gz | 554.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f7i.ent.gz | 458.2 KB | Display | PDB format |
PDBx/mmJSON format | 4f7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/4f7i ftp://data.pdbj.org/pub/pdb/validation_reports/f7/4f7i | HTTPS FTP |
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-Related structure data
Related structure data | 2y41S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38398.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: leuB, TTHA1230 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase |
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-Non-polymers , 8 types, 497 molecules
#2: Chemical | ChemComp-IPM / #3: Chemical | ChemComp-NAD / #4: Chemical | #5: Chemical | ChemComp-MN / #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-EOH / #9: 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: 2.18 Å3/Da / Density % sol: 43.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 % PEG 6000, 10 % ethanol, 0.1 M MOPS-K pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2011 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2→48 Å / Num. all: 175413 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.12 Å / Mean I/σ(I) obs: 1.92 / Num. unique all: 27157 / Rsym value: 0.42 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y41 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.475 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 32.392 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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