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- PDB-1o6z: 1.95 A resolution structure of (R207S,R292S) mutant of malate deh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o6z | ||||||
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Title | 1.95 A resolution structure of (R207S,R292S) mutant of malate dehydrogenase from the halophilic archaeon Haloarcula marismortui (holo form) | ||||||
![]() | MALATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / HALOPHILIC / ION-BINDING / PROTEIN-SOLVENT INTERACTION / MALATE DEHYDROGENASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Irimia, A. / Ebel, C. / Madern, D. / Richard, S.B. / Cosenza, L.W. / Zaccai, G. / Vellieux, F.M.D. | ||||||
![]() | ![]() 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. / Vellieux, F.M.D. #1: Journal: Biochemistry / Year: 2000 Title: Insights Into the Molecular Relationships between Malate and Lactate Dehydrogenases: Structural and Biochemical Properties of Monomeric and Dimeric Intermediates of a Mutant of Tetrameric L- ...Title: Insights Into the Molecular Relationships between Malate and Lactate Dehydrogenases: Structural and Biochemical Properties of Monomeric and Dimeric Intermediates of a Mutant of Tetrameric L-[Ldh-Like] Malate Dehydrogenase from the Halophilic Archaeon Haloarcula Marismortui Authors: Madern, D. / Ebel, C. / Mevarech, M. / Richard, S.B. / Pfister, C. / Zaccai, G. #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. #4: Journal: Eur.J.Biochem. / Year: 1995 Title: Mutation at a Single Acidic Amino Acid Enhances the Halophilic Behaviour of Malate Dehydrogenase from Haloarcula Marismortui in Physiological Salts Authors: Madern, D. / Pfister, C. / Zaccai, G. #5: 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 254.5 KB | Display | ![]() |
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PDB format | ![]() | 205.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2x0rC ![]() 1gt2 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 32566.301 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH NADH / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 62.41 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.6 / Details: 2 M NACL, 25 MM TRIS PH 7.6, 2.5 MM NADH, 50% MPD | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 17, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.26 Å / Num. obs: 100475 / % possible obs: 77.8 % / Observed criterion σ(I): 0 / Redundancy: 3.34 % / Biso Wilson estimate: 18.84 Å2 / Rmerge(I) obs: 0.0642 / Net I/σ(I): 12.86 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.12 % / Rmerge(I) obs: 0.1427 / Mean I/σ(I) obs: 4.03 / % possible all: 43.9 |
Reflection | *PLUS Num. measured all: 335871 |
Reflection shell | *PLUS % possible obs: 43.9 % / Num. unique obs: 5703 / Num. measured obs: 12111 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GT2 ![]() 1gt2 Resolution: 1.95→12 Å / SU B: 6.089 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.17 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE REGION 100-107 OF B AND D CHAIN IS DISORDERED. THE RESIDUES 101-106 IN THESE DISORDERED REGIONS COULD NOT BE MODELLED AND ARE OMITTED FROM THE MODEL.
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Displacement parameters | Biso mean: 24.478 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→12 Å
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Refinement | *PLUS Lowest resolution: 42.26 Å / Num. reflection obs: 95398 / Num. reflection Rfree: 5076 / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.955 Å / Lowest resolution: 2.005 Å / Rfactor Rfree: 0.311 / % reflection Rfree: 204 % / Rfactor Rwork: 0.213 / Num. reflection Rwork: 4065 / Total num. of bins used: 20 |