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Yorodumi- PDB-3vkz: 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vkz | ||||||
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Title | 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at atmospheric pressure | ||||||
Components | 3-isopropylmalate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 3-ISOPROPYLMALATE DEHYDROGENASE / IPMDH / HIGH-PRESSURE / DIAMOND-ANVIL CELL / DAC | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / amino acid biosynthetic process / NAD binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Nagae, T. / Watanabe, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase Authors: Nagae, T. / Kawamura, T. / Chavas, L.M.G. / Niwa, K. / Hasegawa, M. / Kato, C. / Watanabe, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vkz.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vkz.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vkz_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 3vkz_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 3vkz_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 3vkz_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/3vkz ftp://data.pdbj.org/pub/pdb/validation_reports/vk/3vkz | HTTPS FTP |
-Related structure data
Related structure data | 3vl2C 3vl3C 3vl4C 3vl6C 3vl7C 1a05S 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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Unit cell |
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-Components
#1: Protein | Mass: 40689.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: leuB, SO_4235 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplus(de3) Ril References: UniProt: Q8E9N3, 3-isopropylmalate dehydrogenase |
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#2: Chemical | ChemComp-IPM / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-CL / |
#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: 2.63 Å3/Da / Density % sol: 53.3 % / Mosaicity: 0.458 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, calcium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 25, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.84→50 Å / Num. obs: 31951 / % possible obs: 89.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Χ2: 2.921 / Net I/σ(I): 21.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A05 Resolution: 1.84→22.15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.161 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.72 Å2 / Biso mean: 26.2431 Å2 / Biso min: 9.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→22.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.838→1.885 Å / Total num. of bins used: 20
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