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- PDB-7f8d: Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)... -

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Basic information

Entry
Database: PDB / ID: 7f8d
TitleMalate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) G218Y mutant
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Malate Dehydrogenase
Function / homology
Function and homology information


(S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / tricarboxylic acid cycle / nucleotide binding
Similarity search - Function
Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 ...Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShimozawa, Y. / Himiyama, T. / Nakamura, T. / Nishiya, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06616 Japan
Japan Society for the Promotion of Science (JSPS)20K15403 Japan
Japan Society for the Promotion of Science (JSPS)20K05740 Japan
CitationJournal: Protein Eng.Des.Sel. / Year: 2021
Title: Increasing loop flexibility affords low-temperature adaptation of a moderate thermophilic malate dehydrogenase from Geobacillus stearothermophilus.
Authors: Shimozawa, Y. / Himiyama, T. / Nakamura, T. / Nishiya, Y.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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)146,8078
Polymers144,1544
Non-polymers2,6544
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20410 Å2
ΔGint-98 kcal/mol
Surface area42560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.424, 110.220, 150.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Malate dehydrogenase


Mass: 36038.434 Da / Num. of mol.: 4 / Mutation: G218Y
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, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 mM Tris-HCl (pH 7.0), 12% PEG 8000, 0.2 M magnesium chloride, 2 mM oxaloacetic acid, 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: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.51 Å / Num. obs: 51272 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.6
Reflection shellResolution: 2.4→2.47 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 4381 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BY8

7by8


Resolution: 2.4→48.509 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.224 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.284
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2579 2625 5.126 %
Rwork0.1795 48582 -
all0.184 --
obs-51207 99.975 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 50.407 Å2
Baniso -1Baniso -2Baniso -3
1-0.044 Å2-0 Å20 Å2
2--0.002 Å2-0 Å2
3----0.046 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9520 0 176 204 9900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139850
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179700
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.64713362
X-RAY DIFFRACTIONr_angle_other_deg1.2661.5822380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18251246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53323.005426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58151750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5681552
X-RAY DIFFRACTIONr_chiral_restr0.0690.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022002
X-RAY DIFFRACTIONr_nbd_refined0.2010.21926
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.28942
X-RAY DIFFRACTIONr_nbtor_refined0.1590.24809
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.211
X-RAY DIFFRACTIONr_nbd_other0.210.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.26
X-RAY DIFFRACTIONr_mcbond_it4.2465.0634996
X-RAY DIFFRACTIONr_mcbond_other4.2455.0624995
X-RAY DIFFRACTIONr_mcangle_it5.6817.5836238
X-RAY DIFFRACTIONr_mcangle_other5.6817.5846239
X-RAY DIFFRACTIONr_scbond_it5.395.6464854
X-RAY DIFFRACTIONr_scbond_other5.3895.6464855
X-RAY DIFFRACTIONr_scangle_it7.6068.2357124
X-RAY DIFFRACTIONr_scangle_other7.6068.2357125
X-RAY DIFFRACTIONr_lrange_it9.22560.12910551
X-RAY DIFFRACTIONr_lrange_other9.22660.13110550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.2812170.1835070.18637240.8950.9221000.159
2.462-2.5290.2751800.16134670.16636470.9040.9381000.142
2.529-2.6030.2561490.16833820.17235310.9110.9311000.147
2.603-2.6820.2731800.17832550.18334350.8920.9241000.156
2.682-2.770.2681560.17931680.18333240.9180.9241000.158
2.77-2.8670.2981690.17530710.18132400.8910.9281000.155
2.867-2.9750.281450.17729970.18131420.8840.9311000.158
2.975-3.0960.2721620.19828280.20229900.8990.9171000.182
3.096-3.2330.2971550.20127400.20628950.8860.9211000.185
3.233-3.390.2931370.20526200.20927570.90.9231000.193
3.39-3.5720.2691280.18925030.19326310.9170.9461000.18
3.572-3.7880.2391250.18123820.18425100.9370.95299.88050.174
3.788-4.0480.231250.1722450.17423710.9450.95599.95780.163
4.048-4.3690.2331150.1620790.16321940.9360.9571000.155
4.369-4.7820.211290.14619350.1520640.9520.9651000.144
4.782-5.3410.21910.15517540.15818450.9580.9661000.152
5.341-6.1540.289830.1915780.19416610.920.9491000.181
6.154-7.5070.25660.17213550.17514210.9370.9551000.167
7.507-10.4920.224790.16210480.16611270.9530.971000.161
10.492-48.5090.341340.3236680.3247020.7930.7991000.308

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