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Yorodumi- PDB-1ai3: ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ai3 | ||||||
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Title | ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES | ||||||
Components | ISOCITRATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / NADP / PHOSPHORYLATION / GLYOXYLATE BYPASS | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / tricarboxylic acid cycle / electron transport chain / NAD binding / response to oxidative stress / magnesium ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Stoddard, B.L. / Mesecar, A. / Koshland Junior, D.E. | ||||||
Citation | Journal: Science / Year: 1997 Title: Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Authors: Mesecar, A.D. / Stoddard, B.L. / Koshland Jr., D.E. #1: Journal: Biochemistry / Year: 1996 Title: Determinants of Cofactor Specificity in Isocitrate Dehydrogenase: Structure of an Engineered Nadp+--> Nad+ Specificity-Reversal Mutant Authors: Hurley, J.H. / Chen, R. / Dean, A.M. #2: Journal: Biochemistry / Year: 1993 Title: Structure of Isocitrate Dehydrogenase with Isocitrate, Nicotinamide Adenine Dinucleotide Phosphate, and Calcium at 2.5-A Resolution: A Pseudo-Michaelis Ternary Complex Authors: Stoddard, B.L. / Dean, A. / Koshland Junior, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ai3.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ai3.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ai3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/1ai3 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/1ai3 | HTTPS FTP |
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-Related structure data
Related structure data | 1ai2C 1isoS S: Starting model for refinement C: citing same article (ref.) |
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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: 45809.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: DEK2004 / Plasmid: PICD / Production host: Escherichia coli (E. coli) References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-NDO / |
#3: Chemical | ChemComp-ICT / |
#4: Chemical | ChemComp-MG / |
#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: 4.31 Å3/Da / Density % sol: 71.46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 / Method: unknownDetails: Hurley, J.H., (1989) Proc. Natl. Acad. Sci. U.S.A., 86, 8635. | ||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12C / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996 / Details: TORROIDAL MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 62143 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.18 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 198342 / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ISO Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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