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- PDB-1guy: Structural Basis for Thermophilic Protein Stability: Structures o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1guy | ||||||
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Title | Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases | ||||||
![]() | MALATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / DEHYDROGENASE / TRICARBOXYLIC ACID CYCLE / NAD | ||||||
Function / homology | ![]() malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.1 KB | Display | ![]() |
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PDB format | ![]() | 102 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 992.6 KB | Display | ![]() |
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Full document | ![]() | 1004.1 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1guzC ![]() 1gv0C ![]() 1gv1C ![]() 1ldbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32747.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 5-15% PEG400, 100 MM NAAC, PH 4.6, 40MM 5-15% PEG400, 100 MM NAAC, PH 4.6, 40MM CDAC | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 35062 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.124 |
Reflection shell | Resolution: 2.2→2.33 Å / Rmerge(I) obs: 0.284 / % possible all: 87.1 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 80712 |
Reflection shell | *PLUS % possible obs: 87.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MODIFICATION OF PDB ENTRY 1LDB Resolution: 2.2→19.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2919001.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.146 Å2 / ksol: 0.353051 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 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: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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