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- PDB-2j5k: 2.0 A resolution structure of the wild type malate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 2j5k
Title2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / 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
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 ...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
Malate dehydrogenase
Similarity search - Component
Biological speciesHALOARCULA MARISMORTUI (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFioravanti, 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
DepositionSep 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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)131,63512
Polymers131,3514
Non-polymers2848
Water18,4291023
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)127.151, 114.240, 124.141
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MALATE DEHYDROGENASE /


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 / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1023 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.11 %
Crystal growMethod: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 4, 2005 / Details: MIRRORS
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O6Z

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 5643 4.7 %RANDOM
Rwork0.2252 ---
obs0.2252 112033 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.2269 Å2 / ksol: 0.380188 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.96 Å20 Å2-0.158 Å2
2--1.841 Å20 Å2
3---6.118 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9052 0 8 1023 10083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012053
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.52954
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.38
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.0911.5
X-RAY DIFFRACTIONc_mcangle_it3.2492
X-RAY DIFFRACTIONc_scbond_it2.7782
X-RAY DIFFRACTIONc_scangle_it4.112.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3105 518 4.36 %
Rwork0.2671 9568 -
obs--84.87 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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