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- PDB-9s3k: Crystal structure of ancestral (Methanocaldococcaceae/A34) Malate... -

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Basic information

Entry
Database: PDB / ID: 9s3k
TitleCrystal structure of ancestral (Methanocaldococcaceae/A34) Malate dehydrogenase
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Malate dehydrogenase / NADP binding domain
Function / homology: / Chem-NDP
Function and homology information
Biological speciesMethanocaldococcaceae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCoquille, S. / Madern, D.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE44-0034-01 France
Agence Nationale de la Recherche (ANR)ANR-22-CE02-0027 France
CitationJournal: J.Mol.Biol. / Year: 2026
Title: Unraveling the link between thermal adaptation and latent allostery in malate dehydrogenase from Methanococcales
Authors: Simoes Pereira, C. / Coquille, S. / Brochier-Armanet, C. / Sterpone, F. / Madern, D.
History
DepositionJul 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 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
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,29412
Polymers138,1564
Non-polymers3,1388
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20930 Å2
ΔGint-54 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.904, 102.990, 129.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Malate dehydrogenase


Mass: 34538.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Ancestral sequence of Methanocaldococcaceae MalDH reconstructed using BPPANCESTOR
Source: (gene. exp.) Methanocaldococcaceae (archaea)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: malate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium citrate dibasic, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.979507 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979507 Å / Relative weight: 1
ReflectionResolution: 2.508→80.691 Å / Num. obs: 27491 / % possible obs: 92.64 % / Redundancy: 13.1 % / Biso Wilson estimate: 38.65 Å2 / CC1/2: 0.9913 / Rmerge(I) obs: 0.385 / Rpim(I) all: 0.11 / Rrim(I) all: 0.4 / Net I/σ(I): 7.065
Reflection shellResolution: 2.508→2.753 Å / Rmerge(I) obs: 1.806 / Mean I/σ(I) obs: 1.523 / Num. unique obs: 1376 / CC1/2: 0.5632 / Rpim(I) all: 0.521 / Rrim(I) all: 1.882

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
AutoProcessdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→80.69 Å / SU ML: 0.2901 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 1295 4.88 %
Rwork0.1985 25265 -
obs0.2009 26560 76.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.45 Å2
Refinement stepCycle: LAST / Resolution: 2.7→80.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9521 0 196 103 9820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729858
X-RAY DIFFRACTIONf_angle_d0.811513345
X-RAY DIFFRACTIONf_chiral_restr0.04891577
X-RAY DIFFRACTIONf_plane_restr0.00581689
X-RAY DIFFRACTIONf_dihedral_angle_d15.2963667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.3184390.25341020X-RAY DIFFRACTION28.19
2.81-2.940.3262740.27621491X-RAY DIFFRACTION41.31
2.94-3.090.2914970.26492002X-RAY DIFFRACTION55.63
3.09-3.280.3121410.23482624X-RAY DIFFRACTION72.72
3.28-3.540.26021840.21893336X-RAY DIFFRACTION91.93
3.54-3.890.26182030.20023571X-RAY DIFFRACTION99.97
3.89-4.460.2241780.15953683X-RAY DIFFRACTION99.97
4.46-5.620.2341790.1813694X-RAY DIFFRACTION99.9
5.62-80.690.21932000.1913844X-RAY DIFFRACTION99.63

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