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- PDB-6itl: Crystal structure of malate dehydrogenase from Mannheimia succini... -

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Basic information

Entry
Database: PDB / ID: 6itl
TitleCrystal structure of malate dehydrogenase from Mannheimia succiniciproducens in complex with NAD
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / nucleotide binding
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 ...Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesMannheimia succiniciproducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2813
Polymers33,5261
Non-polymers7562
Water2,486138
1
A: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5626
Polymers67,0512
Non-polymers1,5114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area6050 Å2
ΔGint-38 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.089, 80.089, 193.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

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Components

#1: Protein Malate dehydrogenase


Mass: 33525.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mannheimia succiniciproducens (strain MBEL55E) (bacteria)
Strain: MBEL55E / Gene: mdh, MS1266 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q65T37, malate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, Tacsimate

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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 17, 2017
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: 1.97→34.03 Å / Num. obs: 26683 / % possible obs: 99.7 % / Redundancy: 11.7 % / CC1/2: 0.988 / Rmerge(I) obs: 0.072 / Net I/σ(I): 54.6
Reflection shellResolution: 1.97→2.01 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 11 / Num. unique obs: 1321 / CC1/2: 0.952 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BAL

6bal


Resolution: 1.97→34.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.168 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.136
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1410 5.3 %RANDOM
Rwork0.1717 ---
obs0.1741 25239 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.99 Å2 / Biso mean: 26.079 Å2 / Biso min: 15.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å2-0 Å2
2---0.36 Å2-0 Å2
3---1.15 Å2
Refinement stepCycle: final / Resolution: 1.97→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 50 138 2465
Biso mean--26.59 31.21 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172311
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6333205
X-RAY DIFFRACTIONr_angle_other_deg1.4451.5725354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31123.48389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21115397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3291510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
LS refinement shellResolution: 1.969→2.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 89 -
Rwork0.203 1699 -
all-1788 -
obs--92.12 %

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