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- PDB-6ihe: Crystal structure of Malate dehydrogenase from Metallosphaera sedula -

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Basic information

Entry
Database: PDB / ID: 6ihe
TitleCrystal structure of Malate dehydrogenase from Metallosphaera sedula
ComponentsMalate dehydrogenase (NAD)
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Malate dehydrogenase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, D. / Kim, K.J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula
Authors: Lee, D. / Hong, J. / Kim, K.J.
History
DepositionSep 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 (NAD)
B: Malate dehydrogenase (NAD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,67821
Polymers66,2982
Non-polymers3,37919
Water4,071226
1
A: Malate dehydrogenase (NAD)
B: Malate dehydrogenase (NAD)
hetero molecules

A: Malate dehydrogenase (NAD)
B: Malate dehydrogenase (NAD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,35542
Polymers132,5974
Non-polymers6,75838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area12840 Å2
ΔGint-52 kcal/mol
Surface area43440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.194, 134.194, 81.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Malate dehydrogenase (NAD)


Mass: 33149.242 Da / Num. of mol.: 2 / Fragment: UNP residues 2-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula (archaea) / Gene: Msed_0455 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_T1R(DE3) / References: UniProt: A0A088E2H7, malate dehydrogenase

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Non-polymers , 8 types, 245 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.21 Å3/Da / Density % sol: 61.71 % / Mosaicity: 0.678 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 40 % (v/v) polyethylene glycol (PEG) 300, 0.1 M CHES / sodium hydroxide pH 9.5, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 17, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 65061 / % possible obs: 96.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Χ2: 1.97 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.934.40.33332320.7540.1620.3731.0397.4
1.93-1.974.50.31532280.8030.1510.3521.11696.7
1.97-2.014.80.2832390.8970.1280.311.23396.7
2.01-2.0550.27632170.8960.1240.3051.24196.7
2.05-2.095.10.25131940.9260.110.2751.28795.9
2.09-2.145.60.22332480.950.0930.2431.44897.5
2.14-2.195.60.20332360.9650.0830.2211.48696.4
2.19-2.255.90.18232150.9740.0730.1971.52296.9
2.25-2.326.30.16732210.9810.0650.181.58595.9
2.32-2.396.40.14631880.9880.0550.1571.68995.1
2.39-2.486.60.13632080.9890.0510.1461.72595.9
2.48-2.586.80.12232020.9920.0450.131.85195.3
2.58-2.77.30.10732110.9940.0380.1141.88196.3
2.7-2.847.60.09832270.9950.0350.1041.94895.4
2.84-3.0280.08432300.9960.0290.0892.08796.1
3.02-3.258.40.07732730.9970.0260.0812.25297
3.25-3.5890.06633230.9980.0210.0692.51197.6
3.58-4.099.50.05833200.9980.0190.0612.68498.1
4.09-5.169.60.05433720.9980.0180.0572.75398.2
5.16-509.10.05234770.9960.0180.0552.77998

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.139 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 3181 4.9 %RANDOM
Rwork0.1922 ---
obs0.1938 61878 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.44 Å2 / Biso mean: 36.481 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 220 226 5098
Biso mean--49.71 42.65 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194949
X-RAY DIFFRACTIONr_bond_other_d0.0020.024879
X-RAY DIFFRACTIONr_angle_refined_deg1.9772.0076646
X-RAY DIFFRACTIONr_angle_other_deg1.067311295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5815604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33325.055182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93315872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0091518
X-RAY DIFFRACTIONr_chiral_restr0.1190.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215306
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02990
LS refinement shellResolution: 1.898→1.947 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 217 -
Rwork0.439 4526 -
all-4743 -
obs--95.78 %

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