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- PDB-2j5q: 2.15 A resolution structure of the wild type malate dehydrogenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j5q | ||||||
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Title | 2.15 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after first radiation burn (radiation damage series) | ||||||
![]() | MALATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / NAD / HALOPHILE / RADIATION DAMAGE / MALATE DEHYDROGENASE / TRICARBOXYLIC ACID CYCLE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Fioravanti, E. / Vellieux, F.M.D. / Amara, P. / Madern, D. / Weik, M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() Title: Structural Features that Stabilize Halophilic Malate-Dehydrogenase from an Archaebacterium. Authors: Dym, O. / Mevarech, M. / Sussman, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253 KB | Display | ![]() |
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PDB format | ![]() | 203.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2j5kC ![]() 2j5rC ![]() 1o6zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32837.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 63 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.15→20 Å / Num. obs: 91779 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 11.88 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O6Z Resolution: 2.15→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.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.6764 Å2 / ksol: 0.381275 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.23 Å / Total num. of bins used: 10
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