[English] 日本語
Yorodumi- PDB-1d3a: CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d3a | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM | ||||||
Components | HALOPHILIC MALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD AND 3 SORTS OF COMPLEX SALT BRIDGES | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.94 Å | ||||||
Authors | Richard, S.B. / Madern, D. / Garcin, E. / Zaccai, G. | ||||||
Citation | Journal: Biochemistry / Year: 2000 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: Journal: ARCHAEA : A LABORATORY MANUAL. V.[1]. HALOPHILES / Year: 1995 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: Journal: Science / Year: 1995 Title: Structural Features Stabilizing Halophilic Malate Dehydrogenase from an Archaebacterium Authors: Dym, O. / Mevarech, M. / Sussman, J.L. #3: Journal: Eur.J.Biochem. / Year: 1995 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: Journal: Biochemistry / Year: 1993 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1d3a.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d3a.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d3a ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d3a | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32706.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloarcula marismortui (Halophile) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: Q07841, malate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.24 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 284 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→30 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.94→3.04 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
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
|