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Yorodumi- PDB-2uxr: Complex with isocitrate and the protein isocitrate dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uxr | ||||||
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Title | Complex with isocitrate and the protein isocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila | ||||||
Components | ISOCITRATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / PSYCHROPHILIC / COLD ADAPTATION / THERMAL STABILITY / ISOCITRATE DEHYDROGENASE | ||||||
Function / homology | Function and homology information isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / tricarboxylic acid cycle / peroxisome / NAD binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | DESULFOTALEA PSYCHROPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Fedoy, A.-E. / Yang, N. / Martinez, A. / Leiros, H.-K.S. / Steen, I.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural and Functional Properties of Isocitrate Dehydrogenase from the Psychrophilic Bacterium Desulfotalea Psychrophila Reveal a Cold -Active Enzyme with an Unusual High Thermal Authors: Fedoy, A.-E. / Yang, N. / Martinez, A. / Leiros, H.-K.S. / Steen, I.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uxr.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uxr.ent.gz | 137.2 KB | Display | PDB format |
PDBx/mmJSON format | 2uxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/2uxr ftp://data.pdbj.org/pub/pdb/validation_reports/ux/2uxr | HTTPS FTP |
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-Related structure data
Related structure data | 2uxqSC 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: 45649.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOTALEA PSYCHROPHILA (bacteria) Description: ICD-11 DADR1 TRPA62 TRPE61 TNA-5 LAMBDA-) LYSOGENIZED BY (LAMBDA)DE3 Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6AQ66 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.7 Å3/Da / Density % sol: 53.7 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 100 MM TRIS/HCL BUFFER PH 7.4, 1.7-1.9 M AMMONIUM SULPHATE, 2% PEG 400, 6 0 MM MGSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 44111 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UXQ Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.028 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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