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- PDB-1o6z: 1.95 A resolution structure of (R207S,R292S) mutant of malate deh... -

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Basic information

Entry
Database: PDB / ID: 1o6z
Title1.95 A resolution structure of (R207S,R292S) mutant of malate dehydrogenase from the halophilic archaeon Haloarcula marismortui (holo form)
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / HALOPHILIC / ION-BINDING / PROTEIN-SOLVENT INTERACTION / MALATE DEHYDROGENASE
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
: / Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal ...: / Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesHALOARCULA MARISMORTUI (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsIrimia, A. / Ebel, C. / Madern, D. / Richard, S.B. / Cosenza, L.W. / Zaccai, G. / Vellieux, F.M.D.
Citation
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. / 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: 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.
#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
DepositionOct 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
C: MALATE DEHYDROGENASE
D: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,20316
Polymers130,2654
Non-polymers2,93712
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.640, 114.420, 124.870
Angle α, β, γ (deg.)90.00, 93.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2056-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99635, -0.084004, -0.015169), (-0.081693, 0.886791, 0.454893), (-0.024761, 0.454471, -0.890417)55.65631, -11.70613, 58.82204
2given(0.993927, 0.06586, 0.08816), (0.065578, -0.997829, 0.006093), (0.08837, -0.000274, -0.996088)-2.73505, -1.78311, 59.14408
3given(-0.997705, 0.01657, -0.065642), (0.015789, -0.8859, -0.463607), (-0.065834, -0.46358, 0.883606)56.88684, 13.81413, 5.43093
4given(-0.997866, 0.016972, -0.063046), (0.013663, -0.889958, -0.455837), (-0.063845, -0.455726, 0.887827)56.75201, 13.61702, 5.10483
5given(0.994406, 0.067311, 0.081389), (0.067865, -0.997686, -0.004053), (0.080928, 0.009554, -0.996674)-2.42347, -2.17316, 59.48046
6given(-0.996524, -0.081403, -0.017663), (-0.080407, 0.884688, 0.459195), (-0.021752, 0.459019, -0.888159)55.33687, -11.94307, 58.76286

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Components

#1: Protein
MALATE DEHYDROGENASE / MDH


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.) HALOARCULA MARISMORTUI (Halophile) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q07841, malate dehydrogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ARG 188 SER AND ARG 267 SER IN CHAINS A, B, C AND D

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 62.41 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES1droppH7.6
24 M1dropNaCl
320 mg/mlprotein1drop
462 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameClassification
REFMACrefinement
XDSdata reduction
BIOMOLdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GT2

1gt2
PDB Unreleased entry


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.
RfactorNum. reflection% reflectionSelection details
Rfree0.26328 5049 5.1 %RANDOM
Rwork0.18991 ---
obs0.19365 94883 78.8 %-
Displacement parametersBiso mean: 24.478 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20.75 Å2
2--0.36 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 1.95→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 184 677 9949
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.038
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.45
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.8
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

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