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- PDB-9s3y: Crystal structure of ancestral (Methanococcaceae/A19) Malate dehy... -

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Basic information

Entry
Database: PDB / ID: 9s3y
TitleCrystal structure of ancestral (Methanococcaceae/A19) Malate dehydrogenase
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Malate dehydrogenase / NADP binding domain
Function / homologyMALONATE ION / Chem-NDP
Function and homology information
Biological speciesMethanococcales (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: 2025
Title: Unraveling the link between thermal adaptation and latent allostery in malate dehydrogenase from Methanococcales.
Authors: Pereira, C.S. / Coquille, S. / Brochier-Armanet, C. / Sterpone, F. / Madern, D.
History
DepositionJul 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 10, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,39618
Polymers68,6352
Non-polymers2,76116
Water7,855436
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,79336
Polymers137,2704
Non-polymers5,52332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Unit cell
Length a, b, c (Å)189.500, 189.500, 143.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-708-

HOH

31A-710-

HOH

41A-726-

HOH

51A-736-

HOH

61A-742-

HOH

71B-670-

HOH

81B-689-

HOH

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Components

#1: Protein Malate dehydrogenase


Mass: 34317.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ancestral sequence of Methanococcales MalDH reconstructed using BPPANCESTOR
Source: (gene. exp.) Methanococcales (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.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2.7-2.9M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 149702 / % possible obs: 95.9 % / Redundancy: 3.86 % / Biso Wilson estimate: 30.07 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.173 / Net I/σ(I): 8.04
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 11126 / CC1/2: 0.384 / Rrim(I) all: 1.24 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→29.96 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.88 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 7478 5 %
Rwork0.1684 --
obs0.1697 149691 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 0 182 436 5377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045063
X-RAY DIFFRACTIONf_angle_d0.6586850
X-RAY DIFFRACTIONf_dihedral_angle_d14.841898
X-RAY DIFFRACTIONf_chiral_restr0.047786
X-RAY DIFFRACTIONf_plane_restr0.005885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.32222500.30284784X-RAY DIFFRACTION96
2.07-2.10.26692510.28254742X-RAY DIFFRACTION96
2.1-2.120.29762480.27444724X-RAY DIFFRACTION96
2.12-2.150.28992540.27354747X-RAY DIFFRACTION96
2.15-2.180.29362460.26224713X-RAY DIFFRACTION95
2.18-2.210.282490.24774648X-RAY DIFFRACTION95
2.21-2.240.25972520.24744739X-RAY DIFFRACTION95
2.24-2.270.24492500.2324713X-RAY DIFFRACTION95
2.27-2.310.27562370.22484668X-RAY DIFFRACTION95
2.31-2.350.26042420.22564723X-RAY DIFFRACTION95
2.35-2.390.26712510.22524760X-RAY DIFFRACTION97
2.39-2.430.22012590.21274838X-RAY DIFFRACTION97
2.43-2.480.23732520.20774782X-RAY DIFFRACTION97
2.48-2.530.26292530.20134831X-RAY DIFFRACTION97
2.53-2.580.23182560.20164794X-RAY DIFFRACTION97
2.58-2.640.21722530.20094773X-RAY DIFFRACTION97
2.64-2.710.22682590.19264843X-RAY DIFFRACTION97
2.71-2.780.21832510.1884757X-RAY DIFFRACTION97
2.78-2.860.24482470.18464808X-RAY DIFFRACTION97
2.86-2.960.22572450.18184767X-RAY DIFFRACTION97
2.96-3.060.21382560.17744778X-RAY DIFFRACTION97
3.06-3.180.16522560.1554781X-RAY DIFFRACTION97
3.18-3.330.17182560.14754775X-RAY DIFFRACTION97
3.33-3.50.15472490.12954790X-RAY DIFFRACTION96
3.5-3.720.15012470.1214757X-RAY DIFFRACTION96
3.72-4.010.13312420.1134646X-RAY DIFFRACTION94
4.01-4.410.11942370.10264624X-RAY DIFFRACTION94
4.41-5.050.12892430.1044574X-RAY DIFFRACTION92
5.05-6.350.1722450.14444671X-RAY DIFFRACTION95
6.35-29.960.20022420.17444663X-RAY DIFFRACTION94

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