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

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Basic information

Entry
Database: PDB / ID: 7bya
TitleMalate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Adenosine 5'-Diphosphoribose (APR)
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-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
ADENOSINE-5-DIPHOSPHORIBOSE / 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)146,0989
Polymers143,7294
Non-polymers2,3685
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19120 Å2
ΔGint-113 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.327, 103.220, 150.790
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: 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, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
#2: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 7.0), 16 % PEG 2000 MME, 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: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.16 Å / Num. obs: 66776 / % possible obs: 100 % / Redundancy: 27.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 21.8
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 8.1 / Num. unique obs: 4459 / CC1/2: 0.99

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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→49.159 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.185 / SU B: 5.733 / SU ML: 0.148 / Average fsc free: 0.9153 / Average fsc work: 0.9326 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2299 3434 5.148 %
Rwork0.1804 63267 -
all0.183 --
obs-66701 99.988 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 48.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20 Å20 Å2
2---0 Å20 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9375 0 153 250 9778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139669
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179409
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.64713114
X-RAY DIFFRACTIONr_angle_other_deg1.2661.57821831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88651231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93623.141417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.875151718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5351550
X-RAY DIFFRACTIONr_chiral_restr0.0680.21329
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021798
X-RAY DIFFRACTIONr_nbd_refined0.1960.21765
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.28396
X-RAY DIFFRACTIONr_nbtor_refined0.1540.24718
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2303
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0770.24
X-RAY DIFFRACTIONr_nbd_other0.1830.211
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3160.21
X-RAY DIFFRACTIONr_mcbond_it3.5364.994939
X-RAY DIFFRACTIONr_mcbond_other3.5344.994938
X-RAY DIFFRACTIONr_mcangle_it4.5427.4726165
X-RAY DIFFRACTIONr_mcangle_other4.5427.4736166
X-RAY DIFFRACTIONr_scbond_it4.0785.4634730
X-RAY DIFFRACTIONr_scbond_other4.0765.4634730
X-RAY DIFFRACTIONr_scangle_it5.8578.0076949
X-RAY DIFFRACTIONr_scangle_other5.8568.0076950
X-RAY DIFFRACTIONr_lrange_it6.92359.08410268
X-RAY DIFFRACTIONr_lrange_other6.92459.06810256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.2-2.2570.262670.20846040.21148710.9120.9290.19
2.257-2.3190.2612410.20144840.20447250.9050.9270.182
2.319-2.3860.2912580.243430.20546010.90.9220.18
2.386-2.4590.272290.19542860.19945150.9070.9270.177
2.459-2.5390.2592050.18441160.18843210.9160.940.169
2.539-2.6280.2812140.1939810.19441950.8950.9320.176
2.628-2.7270.2841950.18838920.19340870.9060.9350.178
2.727-2.8380.2862110.19737250.20239360.9050.9290.189
2.838-2.9640.2571870.19535760.19837630.9160.9320.189
2.964-3.1080.2531960.20134150.20436110.9160.9290.198
3.108-3.2760.2491660.20232720.20434380.9180.9360.203
3.276-3.4730.2611600.20531160.20832760.9210.940.212
3.473-3.7120.1921770.18128830.18230600.9590.9610.189
3.712-4.0070.21380.17227510.17428890.9490.9590.185
4.007-4.3870.191230.1525200.15226430.9580.9660.168
4.387-4.90.161100.1423280.14124380.8780.8560.161
4.9-5.6480.2161290.16419960.16721250.8590.8670.186
5.648-6.8950.222990.16317670.16618660.9460.9640.18
6.895-9.6570.176820.13113650.13414470.9670.9790.155
9.657-49.1590.206470.2278470.2268940.9630.9560.25

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