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Yorodumi- PDB-1gv0: Structural Basis for Thermophilic Protein Stability: Structures o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gv0 | |||||||||
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Title | Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases | |||||||||
Components | MALATE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / TRICARBOXYLIC ACID / NAD | |||||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle Similarity search - Function | |||||||||
Biological species | CHLOROBIUM TEPIDUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Dalhus, B. / Sarinen, M. / Sauer, U.H. / Eklund, P. / Johansson, K. / Karlsson, A. / Ramaswamy, S. / Bjork, A. / Synstad, B. / Naterstad, K. ...Dalhus, B. / Sarinen, M. / Sauer, U.H. / Eklund, P. / Johansson, K. / Karlsson, A. / Ramaswamy, S. / Bjork, A. / Synstad, B. / Naterstad, K. / Sirevag, R. / Eklund, H. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases Authors: Dalhus, B. / Saarinen, M. / Sauer, U.H. / Eklund, P. / Johansson, K. / Karlsson, A. / Ramaswamy, S. / Bjork, A. / Synstad, B. / Naterstad, K. / Sirevag, R. / Eklund, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gv0.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gv0.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gv0 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gv0 | HTTPS FTP |
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-Related structure data
Related structure data | 1guyC 1guzSC 1gv1C C: citing same article (ref.) S: Starting model for refinement |
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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: 33144.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHLOROBIUM TEPIDUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80039, malate dehydrogenase #2: Chemical | #3: 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: 3.1 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 20MG/ML,50MMTRIS-HCL,PH7.4,55%MPD, 100MMHEPES,PH7.5., pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.4 / 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: MAX II / Beamline: I711 / Wavelength: 0.9831 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9831 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40.8 Å / Num. obs: 28459 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.5→2.64 Å / Rmerge(I) obs: 0.254 / % possible all: 100 |
Reflection | *PLUS % possible obs: 100 % / Num. measured all: 117908 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MDH WITH PDB-CODE 1GUZ Resolution: 2.5→40.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3775346.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.952 Å2 / ksol: 0.371756 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→40.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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