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- PDB-5zi2: MDH3 wild type, nad-form -

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Basic information

Entry
Database: PDB / ID: 5zi2
TitleMDH3 wild type, nad-form
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Malate dehydrogenase / glyoxysome / fatty acid oxidation / MDH3
Function / homology
Function and homology information


NADH regeneration / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / glyoxylate cycle / fatty acid beta-oxidation / peroxisomal matrix / tricarboxylic acid cycle / peroxisome / mRNA binding ...NADH regeneration / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / glyoxylate cycle / fatty acid beta-oxidation / peroxisomal matrix / tricarboxylic acid cycle / peroxisome / mRNA binding / mitochondrion / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 ...Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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
ADENOSINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / Malate dehydrogenase, peroxisomal
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMoriyama, S. / Nishio, K. / Mizushima, T.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae.
Authors: Moriyama, S. / Nishio, K. / Mizushima, T.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0107
Polymers74,7562
Non-polymers1,2545
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-50 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.099, 92.559, 82.114
Angle α, β, γ (deg.)90.00, 99.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Malate dehydrogenase


Mass: 37378.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MDH3, SCKG_0552 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A250W9L1, UniProt: P32419*PLUS, malate dehydrogenase

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Non-polymers , 5 types, 208 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 0.2M MgCl2, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44896 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 22 Å2 / Rpim(I) all: 0.048 / Net I/σ(I): 30.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4 / Rpim(I) all: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLD

1mld


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22977 2246 5 %RANDOM
Rwork0.17526 ---
obs0.17802 42491 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.522 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 79 203 5454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195353
X-RAY DIFFRACTIONr_bond_other_d00.025360
X-RAY DIFFRACTIONr_angle_refined_deg1.9472.0027242
X-RAY DIFFRACTIONr_angle_other_deg3.647312373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96425.248202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79415983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7261522
X-RAY DIFFRACTIONr_chiral_restr0.1160.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215926
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021108
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6522.8122720
X-RAY DIFFRACTIONr_mcbond_other2.6462.8112719
X-RAY DIFFRACTIONr_mcangle_it3.7844.2033400
X-RAY DIFFRACTIONr_mcangle_other3.7864.2053401
X-RAY DIFFRACTIONr_scbond_it3.7293.3732633
X-RAY DIFFRACTIONr_scbond_other3.7283.3732634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6824.8283843
X-RAY DIFFRACTIONr_long_range_B_refined7.31323.0665985
X-RAY DIFFRACTIONr_long_range_B_other7.31323.0695986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 160 -
Rwork0.283 3085 -
obs--97.16 %

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