[English] 日本語
Yorodumi- PDB-2j5k: 2.0 A resolution structure of the wild type malate dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j5k | ||||||
---|---|---|---|---|---|---|---|
Title | 2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series) | ||||||
Components | MALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NAD / HALOPHILE / RADIATION DAMAGE / MALATE DEHYDROGENASE / TRICARBOXYLIC ACID CYCLE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fioravanti, E. / Vellieux, F.M.D. / Amara, P. / Madern, D. / Weik, M. | ||||||
Citation | Journal: J.Synchrotron Radiat. / Year: 2007 Title: Specific Radiation Damage to Acidic Residues and its Relation to Their Chemical and Structural Environment. Authors: Fioravanti, E. / Vellieux, F.M.D. / Amara, P. / Madern, D. / Weik, M. #1: Journal: J.Mol.Biol. / Year: 2003 Title: The Oligomeric States of Haloarcula Marismortui Malate Dehydrogenase are Modulated by Solvent Components as Shown by Crystallographic and Biochemical Studies Authors: Irimia, A. / Ebel, C. / Madern, D. / Richard, S.B. / Cosenza, L.W. / Zaccai, G. / D Vellieux, F.M. #2: 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. #3: Journal: Science / Year: 1995 Title: Structural Features that Stabilize Halophilic Malate-Dehydrogenase from an Archaebacterium. Authors: Dym, O. / Mevarech, M. / Sussman, J.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2j5k.cif.gz | 252.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2j5k.ent.gz | 203.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/2j5k ftp://data.pdbj.org/pub/pdb/validation_reports/j5/2j5k | HTTPS FTP |
---|
-Related structure data
Related structure data | 2j5qC 2j5rC 1o6zS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32837.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HALOARCULA MARISMORTUI (Halophile) / Strain: HMS174 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07841, malate dehydrogenase #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.11 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: 3UL OF PROTEIN PLUS 4UL OF MPD WERE EQUILIBRATED AGAINST 58% MPD VIA THE SITTING DROP REVERSE VAPOUR DIFFUSION TECHNIQUE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 4, 2005 / Details: MIRRORS |
Radiation | Monochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 112033 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 12.851 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / % possible all: 85.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O6Z Resolution: 2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: SIDE CHAINS ATOMS WITHOUT ELECTRON DENSITY APPEARING AT 1 SIGMA LEVEL IN 3MFO-2DFC MAPS WERE REMOVED FROM THE MODEL.RESIDUES IN POSITION 100-107 WERE EXCLUDED FROM THE MODEL OF MONOMERS B ...Details: SIDE CHAINS ATOMS WITHOUT ELECTRON DENSITY APPEARING AT 1 SIGMA LEVEL IN 3MFO-2DFC MAPS WERE REMOVED FROM THE MODEL.RESIDUES IN POSITION 100-107 WERE EXCLUDED FROM THE MODEL OF MONOMERS B AND D BECAUSE DISORDERED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.2269 Å2 / ksol: 0.380188 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|