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- PDB-7by9: Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)... -

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Basic information

Entry
Database: PDB / ID: 7by9
TitleMalate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Malate Dehydrogenase
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 3 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXALOACETATE ION / Malate dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShimozawa, Y. / Nakamura, T. / Himiyama, T. / Nishiya, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06616 Japan
Japan Society for the Promotion of Science (JSPS)19K21133 Japan
CitationJournal: J.Biochem. / Year: 2021
Title: Structural analysis and reaction mechanism of malate dehydrogenase from Geobacillus stearothermophilus.
Authors: Shimozawa, Y. / Himiyama, T. / Nakamura, T. / Nishiya, Y.
History
DepositionApr 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,90712
Polymers143,7294
Non-polymers3,1788
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21280 Å2
ΔGint-96 kcal/mol
Surface area41380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.156, 83.239, 119.477
Angle α, β, γ (deg.)90.000, 93.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Malate dehydrogenase /


Mass: 35932.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mdh / Production host: Escherichia coli (E. coli) / References: UniProt: A0A143T1U9, malate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystal of wild-type gs-MDH prepared in 0.1 M HEPES (pH 7.5), 10 % polyethylene glycol (PEG) 6000 and 5 % 2-Methyl-2,4-pentanediol (MPD) was soaked into the cryo-protectant containing 2 mM OAA and 2 mM NAD+.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 62899 / % possible obs: 99 % / Redundancy: 4.6 % / CC1/2: 0.966 / Rmerge(I) obs: 0.198 / Net I/σ(I): 4
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4635 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BY8

7by8


Resolution: 2.2→39.393 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / SU B: 3.312 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.256
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2848 3047 4.866 %
Rwork0.2235 --
all0.226 --
obs-62624 99.564 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.024 Å2-0 Å2-0.034 Å2
2--0.034 Å2-0 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9332 0 212 34 9578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179392
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.64813134
X-RAY DIFFRACTIONr_angle_other_deg1.1881.57721785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92551225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67623.077416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.495151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0381549
X-RAY DIFFRACTIONr_chiral_restr0.0730.21324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021804
X-RAY DIFFRACTIONr_nbd_refined0.2060.22377
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.210125
X-RAY DIFFRACTIONr_nbtor_refined0.1640.24577
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2333
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.230
X-RAY DIFFRACTIONr_nbd_other0.2340.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.25
X-RAY DIFFRACTIONr_mcbond_it4.2034.5074918
X-RAY DIFFRACTIONr_mcbond_other4.2034.5064917
X-RAY DIFFRACTIONr_mcangle_it5.5376.7456137
X-RAY DIFFRACTIONr_mcangle_other5.5376.7466138
X-RAY DIFFRACTIONr_scbond_it3.8314.6964766
X-RAY DIFFRACTIONr_scbond_other3.8314.6964766
X-RAY DIFFRACTIONr_scangle_it5.0736.9676997
X-RAY DIFFRACTIONr_scangle_other5.0726.9676998
X-RAY DIFFRACTIONr_lrange_it7.31454.21810699
X-RAY DIFFRACTIONr_lrange_other7.31354.22110700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.1112410.0594396X-RAY DIFFRACTION99.8063
2.257-2.3190.1442170.0844268X-RAY DIFFRACTION100
2.319-2.3860.1181930.0684206X-RAY DIFFRACTION99.9773
2.386-2.4590.1521960.0853999X-RAY DIFFRACTION99.8334
2.459-2.540.1942010.1013949X-RAY DIFFRACTION99.7356
2.54-2.6290.2232060.1363779X-RAY DIFFRACTION99.3518
2.629-2.7280.2782110.1813612X-RAY DIFFRACTION99.7912
2.728-2.840.2891890.2153543X-RAY DIFFRACTION100
2.84-2.9660.3171590.253401X-RAY DIFFRACTION99.8317
2.966-3.1110.3771530.2763254X-RAY DIFFRACTION99.8827
3.111-3.2790.3291700.2853066X-RAY DIFFRACTION99.6305
3.279-3.4770.3111470.2812921X-RAY DIFFRACTION99.3202
3.477-3.7170.3411380.2832758X-RAY DIFFRACTION99.7245
3.717-4.0150.3631470.2692541X-RAY DIFFRACTION99.9257
4.015-4.3980.2751280.2392346X-RAY DIFFRACTION100
4.398-4.9160.2991040.2172148X-RAY DIFFRACTION99.5579
4.916-5.6750.302770.2541902X-RAY DIFFRACTION99.6475
5.675-6.9460.302780.2551620X-RAY DIFFRACTION98.951
6.946-9.8070.268490.2271235X-RAY DIFFRACTION98.3908
9.807-39.3930.274430.262634X-RAY DIFFRACTION88.9619

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