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- PDB-6itk: Crystal structure of malate dehydrogenase from Corynebacterium gl... -

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Basic information

Entry
Database: PDB / ID: 6itk
TitleCrystal structure of malate dehydrogenase from Corynebacterium glutamicum ATCC 13032 in complex with NAD and malate
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


(S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 2 / 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 Rossmann-like Domain ...Malate dehydrogenase, type 2 / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeo, H. / Kim, K.-J.
CitationJournal: Nat Commun / Year: 2020
Title: Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase.
Authors: Ahn, J.H. / Seo, H. / Park, W. / Seok, J. / Lee, J.A. / Kim, W.J. / Kim, G.B. / Kim, K.J. / Lee, S.Y.
History
DepositionNov 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,6176
Polymers72,0222
Non-polymers1,5954
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-26 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.931, 116.940, 66.003
Angle α, β, γ (deg.)90.000, 95.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

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Components

#1: Protein Malate dehydrogenase


Mass: 36011.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: mdh, Cgl2380, cg2613 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8NN33, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2016
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→77.08 Å / Num. obs: 50050 / % possible obs: 96.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 18
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 2392 / CC1/2: 0.792 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVO

4tvo


Resolution: 2→26.73 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.883 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 2490 5 %RANDOM
Rwork0.1898 ---
obs0.1918 47560 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.39 Å2 / Biso mean: 24.369 Å2 / Biso min: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.31 Å20 Å20.27 Å2
2---0.66 Å2-0 Å2
3----3.64 Å2
Refinement stepCycle: final / Resolution: 2→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 106 229 5109
Biso mean--27.6 30.29 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134968
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174536
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.6356770
X-RAY DIFFRACTIONr_angle_other_deg1.3321.57410490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1625630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00322.791258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46615756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7021534
X-RAY DIFFRACTIONr_chiral_restr0.0730.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
LS refinement shellResolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 193 -
Rwork0.304 3211 -
all-3404 -
obs--88.16 %

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