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- PDB-1d3a: CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENAS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d3a | ||||||
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Title | CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM | ||||||
![]() | HALOPHILIC MALATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / ROSSMANN FOLD AND 3 SORTS OF COMPLEX SALT BRIDGES | ||||||
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 | ![]() ![]() | ||||||
![]() | Richard, S.B. / Madern, D. / Garcin, E. / Zaccai, G. | ||||||
![]() | ![]() Title: Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui. Authors: Richard, S.B. / Madern, D. / Garcin, E. / Zaccai, G. #1: ![]() Title: Protocol 21: the MPD-NACL-H2O System for the Crystallization of Halophilic Proteins Authors: Richard, S.B. / Bonnete, F. / Dym, O. / Zaccai, G. #2: ![]() Title: Structural Features Stabilizing Halophilic Malate Dehydrogenase from an Archaebacterium Authors: Dym, O. / Mevarech, M. / Sussman, J.L. #3: ![]() Title: Mutation at a Single Amino Acid Enhances the Halophilic Behaviour of Malate Dehydrogenase from Haloarcula Marismortui in physiological salts Authors: Madern, D. / Pfister, C. / Zaccai, G. #4: ![]() Title: Cloning, Sequencing, and Expression in Escherichia Coli of the Gene Coding for Malate Dehydrogenase of the Extremely Halophilic Archaebacterium Haloarcula Marismortui Authors: Cendrin, F. / Chroboczek, J. / Zaccai, G. / Eisenberg, H. / Mevarech, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.1 KB | Display | ![]() |
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PDB format | ![]() | 97.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 32706.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.24 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: MPD-NaCl-H2O system, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 284 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→30 Å / Num. obs: 99423 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 82.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 2.94→3.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.332 / Num. unique all: 19960 / % possible all: 94.9 |
Reflection | *PLUS Num. obs: 19960 / Num. measured all: 99423 |
Reflection shell | *PLUS % possible obs: 94.5 % / Num. unique obs: 3237 |
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Processing
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Refinement | Resolution: 2.94→30 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 2600643.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: using maximum likelihood target using amplitudes
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.94→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.94→3.04 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.188 / Num. reflection obs: 15920 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 61.5 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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