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- PDB-5nuf: Cytosolic Malate Dehydrogenase 1 -

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Basic information

Entry
Database: PDB / ID: 5nuf
TitleCytosolic Malate Dehydrogenase 1
ComponentsMalate dehydrogenase 1, cytoplasmic
KeywordsOXIDOREDUCTASE / Dehydrogenase / Malate/Oxaloacetate / NAD+
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / apoplast / malate metabolic process / plant-type vacuole / plasmodesma / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast ...malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / apoplast / malate metabolic process / plant-type vacuole / plasmodesma / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast / mRNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / 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 ...Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / 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
ACETATE ION / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / HYDROGEN PEROXIDE / Malate dehydrogenase 1, cytoplasmic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYoung, D. / Messens, J. / Huang, J. / Reichheld, J.-P.
CitationJournal: J. Exp. Bot. / Year: 2018
Title: Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis.
Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / ...Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / Messens, J. / Reichheld, J.P.
History
DepositionApr 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate dehydrogenase 1, cytoplasmic
B: Malate dehydrogenase 1, cytoplasmic
C: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,26239
Polymers106,8333
Non-polymers4,42936
Water9,620534
1
A: Malate dehydrogenase 1, cytoplasmic
hetero molecules

A: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,36230
Polymers71,2222
Non-polymers3,14028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_577x,-y+2,-z+21
Buried area11030 Å2
ΔGint-158 kcal/mol
Surface area24380 Å2
MethodPISA
2
B: Malate dehydrogenase 1, cytoplasmic
C: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,08124
Polymers71,2222
Non-polymers2,85922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-120 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.592, 118.545, 148.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytsolic malate dehydrogenase 1 / Cytosolic MDH1


Mass: 35610.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: Cytoplasmic / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase

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Non-polymers , 10 types, 570 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.66 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.18 M ammonium sulfate, 0.09 M sodium acetate trihydrate, 27% polyethylene glycol monomethyl ether 2000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen cryogenic stream
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→43.67 Å / Num. obs: 110856 / % possible obs: 94.42 % / Redundancy: 6.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.1717 / Rpim(I) all: 0.07035 / Rrim(I) all: 0.186 / Net I/σ(I): 10.15
Reflection shellResolution: 0.864→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.454 / Rpim(I) all: 0.6292 / Rrim(I) all: 1.252 / % possible all: 67.49

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDH

4mdh


Resolution: 1.8→43.67 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3142 --
Rwork0.1895 --
obs-95355 94.5 %
Refinement stepCycle: LAST / Resolution: 1.8→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7409 0 279 534 8222
LS refinement shellResolution: 1.8→1.864 Å / Rfactor Rfree: 0.3263 / Rfactor Rwork: 0.3142

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