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Yorodumi- PDB-1itw: Crystal structure of the monomeric isocitrate dehydrogenase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1itw | ||||||
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Title | Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and Mn | ||||||
Components | Isocitrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Greece key motif | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, Molecular Replacement method / Resolution: 1.95 Å | ||||||
Authors | Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structure of the Monomeric Isocitrate Dehydrogenase: Evidence of a Protein Monomerization by a Domain Duplication Authors: Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray diffraction studies of monomeric isocitrate dehydrogenase by the MAD method using Mn atoms Authors: Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1itw.cif.gz | 603.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1itw.ent.gz | 491.9 KB | Display | PDB format |
PDBx/mmJSON format | 1itw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1itw ftp://data.pdbj.org/pub/pdb/validation_reports/it/1itw | HTTPS FTP |
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-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: 80507.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: IAM1078 References: UniProt: P16100, isocitrate dehydrogenase (NADP+) #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ICT / #4: 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: 2.6 Å3/Da / Density % sol: 52.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES, PEG6000, glycerol, manganese chloride, DL-isocitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 KDetails: Yasutake, Y., (2001) Acta Crystallogr., Sect.D, 57, 1682. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 20, 2001 |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 237767 / Num. obs: 235314 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 24.474 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.071 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2 / Num. unique all: 33505 / Rsym value: 0.327 / % possible all: 96.7 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 846014 |
Reflection shell | *PLUS % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD, Molecular Replacement method Resolution: 1.95→10 Å / Isotropic thermal model: Isotropic for overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: throughout / Bsol: 69 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5096 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 233612 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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