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- PDB-4wlv: Crystal structure of NAD bound MDH2 -

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Basic information

Entry
Database: PDB / ID: 4wlv
TitleCrystal structure of NAD bound MDH2
ComponentsMalate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / MDH2 / TCA cycle
Function / homology
Function and homology information


malate-aspartate shuttle / L-malate dehydrogenase (NADP+) activity / Malate-aspartate shuttle / Citric acid cycle (TCA cycle) / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle ...malate-aspartate shuttle / L-malate dehydrogenase (NADP+) activity / Malate-aspartate shuttle / Citric acid cycle (TCA cycle) / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / aerobic respiration / gluconeogenesis / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / membrane / nucleus / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Malate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsEo, Y.M. / Han, B.G. / Ahn, H.C.
CitationJournal: To Be Published
Title: Crystal structure of NAD bound MDH2
Authors: Eo, Y.M. / Han, B.G. / Ahn, H.C.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate dehydrogenase, mitochondrial
B: Malate dehydrogenase, mitochondrial
C: Malate dehydrogenase, mitochondrial
D: Malate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,83516
Polymers143,4224
Non-polymers3,41312
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14830 Å2
ΔGint-154 kcal/mol
Surface area43320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.864, 152.016, 155.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Malate dehydrogenase, mitochondrial


Mass: 35855.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P40926, malate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M Na2HPO4:citric acid, 40% (v/v) polyethylene glycol 300, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.4→30.86 Å / Num. obs: 53618 / % possible obs: 99.9 % / Redundancy: 14.3 % / Net I/σ(I): 51.2

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementResolution: 2.4→30.86 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.691 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24787 2863 5.1 %RANDOM
Rwork0.2086 ---
obs0.21057 53618 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.935 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9248 0 216 50 9514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.029628
X-RAY DIFFRACTIONr_bond_other_d0.0020.029504
X-RAY DIFFRACTIONr_angle_refined_deg1.1822.01613108
X-RAY DIFFRACTIONr_angle_other_deg0.7533.00621992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19451252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40625.455308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.606151624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3451528
X-RAY DIFFRACTIONr_chiral_restr0.0520.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021864
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_it1.113.8145020
X-RAY DIFFRACTIONr_mcbond_other1.113.8135019
X-RAY DIFFRACTIONr_mcangle_it1.8715.7156268
X-RAY DIFFRACTIONr_mcangle_other1.8715.7166269
X-RAY DIFFRACTIONr_scbond_it1.2254.0344608
X-RAY DIFFRACTIONr_scbond_other1.2124.0244577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0835.9426793
X-RAY DIFFRACTIONr_long_range_B_refined3.47230.08110265
X-RAY DIFFRACTIONr_long_range_B_other3.46130.04310248
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.397→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 202 -
Rwork0.266 3749 -
obs--97.1 %

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