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- PDB-3ii4: Structure of mycobacterial lipoamide dehydrogenase bound to a tri... -

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Basic information

Entry
Database: PDB / ID: 3ii4
TitleStructure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl inhibitor
ComponentsDihydrolipoyl dehydrogenase
KeywordsOXIDOREDUCTASE / dihydrolipoyl dehydrogenase / DHLDH / E3 / protein-N6-(dihydrolipoyl)lysine / NAD+ oxidoreductase / NAD+ / NADH / Cytoplasm / Disulfide bond / FAD / Flavoprotein / Glycolysis / NAD / Redox-active center
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 / tricarboxylic acid cycle / cell redox homeostasis / glycolytic process / flavin adenine dinucleotide binding / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
FAD dependent oxidoreductase / Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 dependent oxidoreductase / Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3II / FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsLima, C.D.
CitationJournal: Biochemistry / Year: 2010
Title: Triazaspirodimethoxybenzoyls as selective inhibitors of mycobacterial lipoamide dehydrogenase .
Authors: Bryk, R. / Arango, N. / Venugopal, A. / Warren, J.D. / Park, Y.H. / Patel, M.S. / Lima, C.D. / Nathan, C.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,6966
Polymers98,8742
Non-polymers2,8224
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-54 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.900, 98.400, 123.800
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 / Dihydrolipoamide dehydrogenase / E3 component of alpha keto acid dehydrogenase complexes


Mass: 49437.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: expressed as N-terminal His-SUMO fusion protein / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lpd, lpd Rv0462, MT0478, MTV038.06, Rv0462 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL
References: UniProt: P66004, UniProt: P9WHH9*PLUS, dihydrolipoyl dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-3II / N-[2-(2,4-dichlorophenyl)ethyl]-2-{8-[(2,4-dimethoxyphenyl)carbonyl]-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]dec-3-yl}acetamide


Mass: 625.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H34Cl2N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 microM Lpd, 300 microM 3II, 600 microM NADH, 100 mM Tris pH 8.5, 10 mM NaCl, 11% PEG 10000, 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 6, 2008 / Details: Osmic multilayer
RadiationMonochromator: osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 39590 / Num. obs: 39154 / % possible obs: 98.9 % / Observed criterion σ(I): -1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Χ2: 1.522 / Net I/σ(I): 12.7
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.356 / Num. unique all: 3805 / Χ2: 1.284 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOLREPphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A8X

2a8x


Resolution: 2.42→29.66 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2137803 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1942 5 %RANDOM
Rwork0.185 ---
obs-39110 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.569 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 65.72 Å2 / Biso mean: 29.197 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2--5.74 Å20 Å2
3----3.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.42→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6930 0 192 751 7873
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shellResolution: 2.42→2.51 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.311 162 4.5 %
Rwork0.252 3418 -
all-3580 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4in5d.parin5d.top
X-RAY DIFFRACTION5fad_xplor.parfad_xplor.top

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