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Yorodumi- PDB-1cw7: LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-ISOC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cw7 | ||||||
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Title | LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-ISOCITRATE | ||||||
Components | ISOCITRATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / Isocitrate Dehydrogenase / mutant | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / electron transport chain / tricarboxylic acid cycle / NAD binding / response to oxidative stress / magnesium ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Stroud, M.R. / Finer-Moore, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. Authors: Cherbavaz, D.B. / Lee, M.E. / Stroud, R.M. / Koshland Jr., D.E. #1: Journal: Biochemistry / Year: 1991 Title: Catalytic Mechanism of Nadp+-Dependent Isocitrate Dehydrogenase: Implications from the Structures of Magnesium-Isocitrate and Nadp+ Complexes Authors: Hurley, J.H. / Dean, A.M. / Koshland Jr., D.E. / Stroud, R.M. #2: Journal: Biochemistry / Year: 1993 Title: Structure of Isocitrate Dehydrogenase with Isocitrate, Nicotinamide Adenine Phosphate, and Calcium at 2.5-A Resolution: A Pseudo-Michaelis Ternary Complex Authors: Stoddard, B.L. / Dean, A. / Koshland Jr., D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cw7.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cw7.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 1cw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/1cw7 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/1cw7 | HTTPS FTP |
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-Related 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: 45751.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: E. COLI STRAIN JLK1 DEFICIENT IN WILD-TYPE ISOCITRATE DEHYDROGENASE GENE Plasmid: PTK513 / Production host: Escherichia coli (E. coli) References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ICT / |
#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: 4.33 Å3/Da / Density % sol: 71.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: MG-ISOCITRATE, AMMONIUM SULFATE, DTT, NAN3, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→6.87 Å / Num. all: 19141 / Num. obs: 19141 / % possible obs: 75.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.9 |
Reflection | *PLUS Num. measured all: 25364 |
-Processing
Software |
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Refinement | Resolution: 2.6→5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.6→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.58 Å / Lowest resolution: 2.8 Å / Rfactor Rwork: 0.188 |