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- PDB-9qcg: Crystal structure of Methanopyrus kandleri malate dehydrogenase m... -

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Basic information

Entry
Database: PDB / ID: 9qcg
TitleCrystal structure of Methanopyrus kandleri malate dehydrogenase mutant 4 at room temperature
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / Rossmann-like motif / NAD(P)H binding site
Function / homology
Function and homology information


malate dehydrogenase [NAD(P)+] / L-malate dehydrogenase (NADP+) activity / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / tricarboxylic acid cycle
Similarity search - Function
L-lactate dehydrogenase, active site / 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 domain superfamily
Similarity search - Domain/homology
: / Chem-NDP / Malate dehydrogenase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsCoquille, S. / Madern, D.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE44-0034-01 France
CitationJournal: Mol.Biol.Evol. / Year: 2025
Title: Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of an Enzyme Super Family.
Authors: Coquille, S. / Pereira, C.S. / Roche, J. / Santoni, G. / Engilberge, S. / Brochier-Armanet, C. / Girard, E. / Sterpone, F. / Madern, D.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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)70,9819
Polymers69,3062
Non-polymers1,6757
Water2,162120
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,96218
Polymers138,6124
Non-polymers3,35114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18990 Å2
ΔGint-116 kcal/mol
Surface area43260 Å2
Unit cell
Length a, b, c (Å)75.305, 75.305, 270.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

21B-525-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERILEILEAA2 - 3142 - 314
d_12NDPNDPNDPNDPAC401
d_21SERSERILEILEBB2 - 3142 - 314
d_22NDPNDPNDPNDPBG401

NCS oper: (Code: givenMatrix: (-0.999992032861, 2.7752120961E-5, 0.00399167178221), (-3.9341511411E-5, -0.999995784516, -0.00290334341892), (0.00399157438144, -0.00290347732598, 0.999987818502)Vector: ...NCS oper: (Code: given
Matrix: (-0.999992032861, 2.7752120961E-5, 0.00399167178221), (-3.9341511411E-5, -0.999995784516, -0.00290334341892), (0.00399157438144, -0.00290347732598, 0.999987818502)
Vector: -40.1481538822, -40.1720873683, -0.00810028915646)

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Components

#1: Protein Malate dehydrogenase


Mass: 34652.887 Da / Num. of mol.: 2 / Mutation: D51H, R85Q, L146S, S228T, P232I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mdh, MK1069 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TWG5, malate dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium citrate tribasic monohydrate, 17% PEG3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.39→100 Å / Num. obs: 58746 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 47.64 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.648 / Net I/σ(I): 4.19
Reflection shellResolution: 2.39→2.55 Å / Rmerge(I) obs: 4.549 / Mean I/σ(I) obs: 0.43 / Num. unique obs: 10401 / CC1/2: 0.323

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→17.9 Å / SU ML: 0.4085 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.5336
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3089 1564 4.98 %
Rwork0.2627 29823 -
obs0.2651 31387 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.9 Å2
Refinement stepCycle: LAST / Resolution: 2.39→17.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 101 120 4859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224796
X-RAY DIFFRACTIONf_angle_d0.45726514
X-RAY DIFFRACTIONf_chiral_restr0.0442790
X-RAY DIFFRACTIONf_plane_restr0.0035828
X-RAY DIFFRACTIONf_dihedral_angle_d13.26711780
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.676903765272 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.470.39961170.37152449X-RAY DIFFRACTION90.74
2.47-2.550.43881140.36522636X-RAY DIFFRACTION97.31
2.55-2.660.42471270.34492659X-RAY DIFFRACTION98.58
2.66-2.780.32921540.32992694X-RAY DIFFRACTION99.75
2.78-2.920.34311540.30432678X-RAY DIFFRACTION99.82
2.92-3.110.36261550.28692702X-RAY DIFFRACTION99.93
3.11-3.340.35441260.26822748X-RAY DIFFRACTION99.93
3.34-3.680.29521360.24842749X-RAY DIFFRACTION99.65
3.68-4.20.26011680.21882738X-RAY DIFFRACTION99.59
4.2-5.270.26241650.21692791X-RAY DIFFRACTION99.86
5.27-17.90.31031480.26052979X-RAY DIFFRACTION99.74

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