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Yorodumi- PDB-3vba: Crystal structure of methanogen 3-isopropylmalate isomerase small... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vba | ||||||
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Title | Crystal structure of methanogen 3-isopropylmalate isomerase small subunit | ||||||
Components | Isopropylmalate/citramalate isomerase small subunit | ||||||
Keywords | LYASE / LeuD / cytosol | ||||||
Function / homology | Function and homology information maleate hydratase / (R)-2-methylmalate dehydratase / (R)-2-methylmalate dehydratase activity / maleate hydratase activity / 3-isopropylmalate dehydratase / 3-isopropylmalate dehydratase activity / L-leucine biosynthetic process / isoleucine biosynthetic process Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hwang, K.Y. / Lee, E.H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2012 Title: Crystal structure of LeuD from Methanococcus jannaschii. Authors: Lee, E.H. / Cho, Y.W. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vba.cif.gz | 209.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vba.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/3vba ftp://data.pdbj.org/pub/pdb/validation_reports/vb/3vba | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19471.545 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: leuD, MJ1277 / Production host: Escherichia coli (E. coli) References: UniProt: Q58673, 3-isopropylmalate dehydratase, (R)-2-methylmalate dehydratase, maleate hydratase #2: 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: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 25% PEG MME 2000, 0.1M Tris-HCl , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: msc saturna200 / Detector: CCD / Date: Apr 22, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 71994 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.45 Å2 |
Reflection shell | Resolution: 1.98→2.03 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.895 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8467 / SU ML: 0.26 / σ(F): 0.09 / Phase error: 22.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.385 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.8 Å2 / Biso mean: 23.9456 Å2 / Biso min: 6.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.895 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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