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Yorodumi- PDB-1gv1: Structural Basis for Thermophilic Protein Stability: Structures o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gv1 | ||||||
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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 CYCLE / NAD | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / carboxylic acid metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | CHLOROBIUM VIBRIOFORME (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 | 1gv1.cif.gz | 236.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gv1.ent.gz | 192 KB | Display | PDB format |
PDBx/mmJSON format | 1gv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gv1_validation.pdf.gz | 460.8 KB | Display | wwPDB validaton report |
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Full document | 1gv1_full_validation.pdf.gz | 495.4 KB | Display | |
Data in XML | 1gv1_validation.xml.gz | 50.5 KB | Display | |
Data in CIF | 1gv1_validation.cif.gz | 71 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gv1 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gv1 | HTTPS FTP |
-Related structure data
Related structure data | 1guyC 1guzSC 1gv0C 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: 33307.637 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHLOROBIUM VIBRIOFORME (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P80039, UniProt: P0C890*PLUS, malate dehydrogenase #2: Water | ChemComp-HOH / | Sequence details | THE CONFLICT IN SEQUENCE IS CONFIRMED BASED ON THE ELECTRON DENSITY MAP | |
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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: 2.4 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: ~20 MG/ML, 50 MM TRIS-HCL, PH 7.4, 40 % PEG-MME5000, 100 MM | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.92 Å / Num. obs: 37824 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.5 / % possible all: 84.1 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 388140 |
Reflection shell | *PLUS % possible obs: 84.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MDH WITH PDB-CODE 1GUZ Resolution: 2.5→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 267828.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.603 Å2 / ksol: 0.289222 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / 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: 26.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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