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- PDB-7kmy: Structure of Mtb Lpd bound to 010705 -

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Basic information

Entry
Database: PDB / ID: 7kmy
TitleStructure of Mtb Lpd bound to 010705
ComponentsDihydrolipoyl dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / flavoprotein / glycolysis / redox-active center / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Cell redox homeostasis / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / NADH binding / pyruvate dehydrogenase complex / disulfide oxidoreductase activity / zymogen binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / antioxidant activity / Prevention of phagosomal-lysosomal fusion ...Cell redox homeostasis / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / NADH binding / pyruvate dehydrogenase complex / disulfide oxidoreductase activity / zymogen binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / antioxidant activity / Prevention of phagosomal-lysosomal fusion / cell redox homeostasis / flavin adenine dinucleotide binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-WPM / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsLima, C.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA008748 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Whole Cell Active Inhibitors of Mycobacterial Lipoamide Dehydrogenase Afford Selectivity over the Human Enzyme through Tight Binding Interactions.
Authors: Ginn, J. / Jiang, X. / Sun, S. / Michino, M. / Huggins, D.J. / Mbambo, Z. / Jansen, R. / Rhee, K.Y. / Arango, N. / Lima, C.D. / Liverton, N. / Imaeda, T. / Okamoto, R. / Kuroita, T. / Aso, K. ...Authors: Ginn, J. / Jiang, X. / Sun, S. / Michino, M. / Huggins, D.J. / Mbambo, Z. / Jansen, R. / Rhee, K.Y. / Arango, N. / Lima, C.D. / Liverton, N. / Imaeda, T. / Okamoto, R. / Kuroita, T. / Aso, K. / Stamford, A. / Foley, M. / Meinke, P.T. / Nathan, C. / Bryk, R.
History
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _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: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
I: Dihydrolipoyl dehydrogenase
J: Dihydrolipoyl dehydrogenase
M: Dihydrolipoyl dehydrogenase
N: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,30461
Polymers395,4968
Non-polymers12,80753
Water28,1031560
1
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,32918
Polymers98,8742
Non-polymers3,45516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-68 kcal/mol
Surface area31900 Å2
MethodPISA
2
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,05315
Polymers98,8742
Non-polymers3,17913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-66 kcal/mol
Surface area32470 Å2
MethodPISA
3
I: Dihydrolipoyl dehydrogenase
J: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,14516
Polymers98,8742
Non-polymers3,27114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-65 kcal/mol
Surface area32460 Å2
MethodPISA
4
M: Dihydrolipoyl dehydrogenase
N: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,77712
Polymers98,8742
Non-polymers2,90310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-66 kcal/mol
Surface area32550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.506, 178.524, 226.445
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
Dihydrolipoyl dehydrogenase / LPD / Component of peroxynitrite reductase/peroxidase complex / Component of PNR/P / ...LPD / Component of peroxynitrite reductase/peroxidase complex / Component of PNR/P / Dihydrolipoamide dehydrogenase / E3 component of alpha-ketoacid dehydrogenase complexes


Mass: 49437.035 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpdC, lpd, Rv0462, MTV038.06 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WHH9, dihydrolipoyl dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-WPM / N~2~-methyl-N~2~-[(5-methyl-1H-indazol-7-yl)sulfonyl]-N-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)glycinamide


Mass: 389.429 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H19N5O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1560 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Lpd (200 micromolar), inhibitor 13 (300 micromolar) and 600 micromolar NADH were mixed and incubated on ice for 10 min prior to crystallization at 18 C by hanging drop vapor diffusion ...Details: Lpd (200 micromolar), inhibitor 13 (300 micromolar) and 600 micromolar NADH were mixed and incubated on ice for 10 min prior to crystallization at 18 C by hanging drop vapor diffusion against a well solution containing 100 mM Tris pH 8.5, 50 mM NaCl, 15% PEG 10000 (w/v), 14% Glycerol. Crystals were cryo-protected by addition of 25% glycerol and flash-cooled in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.21→113.22 Å / Num. obs: 210765 / % possible obs: 96.9 % / Redundancy: 4.2 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.073 / Rrim(I) all: 0.162 / Net I/σ(I): 10.5
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 19437 / CC1/2: 0.456 / CC star: 0.792 / Rpim(I) all: 0.324 / Rrim(I) all: 0.638 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M52

4m52


Resolution: 2.21→113.22 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 10577 5.01 %
Rwork0.1809 200492 -
obs0.1828 210755 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.6 Å2 / Biso mean: 26.6499 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 2.21→113.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27800 0 862 1560 30222
Biso mean--26.01 29.75 -
Num. residues----3720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229187
X-RAY DIFFRACTIONf_angle_d0.539679
X-RAY DIFFRACTIONf_dihedral_angle_d18.6310264
X-RAY DIFFRACTIONf_chiral_restr0.0434561
X-RAY DIFFRACTIONf_plane_restr0.0035034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.230.27052390.24434559479867
2.23-2.260.28183420.25216587692996
2.26-2.280.28713430.24996620696396
2.28-2.310.28163400.24316596693696
2.31-2.340.26513410.24186673701497
2.34-2.380.27293540.23676597695197
2.38-2.410.28053310.22616604693596
2.41-2.450.26293630.22496622698596
2.45-2.480.26653390.22066576691596
2.48-2.530.24433590.2176382674194
2.53-2.570.24453330.21036714704797
2.57-2.620.24163600.2076713707398
2.62-2.670.2463440.20596763710798
2.67-2.720.24373620.19756712707498
2.72-2.780.24053470.19496753710098
2.78-2.840.23583720.18236758713098
2.84-2.910.22853330.17916779711298
2.91-2.990.21693790.17736740711998
2.99-3.080.20773890.17046759714898
3.08-3.180.23183720.1726754712698
3.18-3.30.2063590.16986623698296
3.3-3.430.21273620.16176841720398
3.43-3.580.18573850.15066852723799
3.58-3.770.17783430.14576848719199
3.77-4.010.18683420.14586933727599
4.01-4.320.18143530.13966894724799
4.32-4.750.16633620.13466906726899
4.75-5.440.18783740.15226985735999
5.44-6.850.22183580.206470907448100
6.85-113.220.22753970.20057259765699

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