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Yorodumi- PDB-1v7l: Structure of 3-isopropylmalate isomerase small subunit from Pyroc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v7l | ||||||
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Title | Structure of 3-isopropylmalate isomerase small subunit from Pyrococcus horikoshii | ||||||
Components | 3-isopropylmalate dehydratase small subunit | ||||||
Keywords | LYASE / BETA BARREL | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydratase / 3-isopropylmalate dehydratase activity / L-leucine biosynthetic process Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å | ||||||
Authors | Yao, M. / Kirita, T. / Sakai, N. / Tanaka, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of the Pyrococcus horikoshii Isopropylmalate Isomerase Small Subunit Provides Insight into the Dual Substrate Specificity of the Enzyme Authors: Yasutake, Y. / Yao, M. / Sakai, N. / Kirita, T. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v7l.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v7l.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 1v7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v7l_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 1v7l_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 1v7l_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1v7l_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/1v7l ftp://data.pdbj.org/pub/pdb/validation_reports/v7/1v7l | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18033.779 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1724 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O59393, 3-isopropylmalate dehydratase #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: 2.52 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.1M HEPES, 1.4M AMMONIUM SULFATE, pH 7.3, 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: BL41XU / Wavelength: 1.045 / Wavelength: 0.979131, 0.979359, 0.97001 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 19, 2000 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.98→25 Å / Num. all: 38097 / Num. obs: 29033 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 15.1 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.082 / Net I/σ(I): 7.1 | |||||||||||||||
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2 / Num. unique all: 4159 / Rsym value: 0.377 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.98→10 Å / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: throughout / Bsol: 55.98 Å2 / ksol: 0.439 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.34 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.1 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: CNS_PROTEIN_REP.PARAM / Topol file: CNS_PROTEIN.TOP |