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Yorodumi- PDB-1hj6: ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hj6 | ||||||
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Title | ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED) | ||||||
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: 2 Å | ||||||
Authors | Doyle, S.A. / Beernink, P.T. / Koshland Junior, D.E. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural Basis for a Change in Substrate Specificity: Crystal Structure of S113E Isocitrate Dehydrogenase in a Complex with Isopropylmalate, Mg2+ and Nadp Authors: Doyle, S.A. / Beernink, P.T. / 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 | 1hj6.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hj6.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hj6_validation.pdf.gz | 830.4 KB | Display | wwPDB validaton report |
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Full document | 1hj6_full_validation.pdf.gz | 848.8 KB | Display | |
Data in XML | 1hj6_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 1hj6_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/1hj6 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/1hj6 | HTTPS FTP |
-Related structure data
Related structure data | |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45851.602 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: ICD / Plasmid: PTK513 / Gene (production host): ICD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JLK1 References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 237 molecules
#2: Chemical | #3: Chemical | ChemComp-IPM / | #4: Chemical | ChemComp-NAP / | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN A CONTAINS ENGINEEREDSequence details | SER 113 TO GLU MUTANT ENZYME | |
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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: 4.43 Å3/Da / Density % sol: 72.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.3 Details: 34-44% (NH4)2SO4, 35MM NA2HPO4, 9 MM CITRIC ACID, 100 MM NACL, 0.2 MM DTT, PH 5.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→21.2 Å / Num. obs: 265721 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.088 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.709 / % possible all: 100 |
Reflection | *PLUS Num. obs: 56218 / % possible obs: 98.8 % / Num. measured all: 265721 / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.709 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IDH-ISOPROPYLMALATE COMPLEX STRUCTURE (A. MESECAR, D.E. KOSHLAND, UNPUBLISHED DATA) Resolution: 2→6 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 34.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.32 |