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- PDB-2a8x: Crystal Structure of Lipoamide Dehydrogenase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 2a8x
TitleCrystal Structure of Lipoamide Dehydrogenase from Mycobacterium tuberculosis
ComponentsDihydrolipoyl dehydrogenase
KeywordsOXIDOREDUCTASE / lipoamide dehydrogenase / pyruvate dehydrogenase / alpha keto acid dehydrogenase
Function / homology
Function and homology information


Cell redox homeostasis / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / NADH binding / disulfide oxidoreductase activity / pyruvate dehydrogenase complex / zymogen binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / antioxidant activity / tricarboxylic acid cycle ...Cell redox homeostasis / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / NADH binding / disulfide oxidoreductase activity / pyruvate dehydrogenase complex / zymogen binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / antioxidant activity / tricarboxylic acid cycle / Prevention of phagosomal-lysosomal fusion / cell redox homeostasis / glycolytic process / flavin adenine dinucleotide binding / extracellular region / plasma membrane / cytosol / cytoplasm
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 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
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsRajashankar, K.R. / Bryk, R. / Kniewel, R. / Buglino, J.A. / Nathan, C.F. / Lima, C.D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure and functional analysis of lipoamide dehydrogenase from Mycobacterium tuberculosis
Authors: Rajashankar, K.R. / Bryk, R. / Kniewel, R. / Buglino, J.A. / Nathan, C.F. / Lima, C.D.
History
DepositionJul 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_conn / struct_keywords / 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 / _refine.pdbx_starting_model / _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,9325
Polymers99,2422
Non-polymers1,6893
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-70 kcal/mol
Surface area32780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.582, 96.677, 122.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Dihydrolipoyl dehydrogenase / E.C.1.8.1.4 / lipoamide dehydrogenase / E3 component of alpha keto acid dehydrogenase complexes / ...lipoamide dehydrogenase / E3 component of alpha keto acid dehydrogenase complexes / Dihydrolipoamide dehydrogenase


Mass: 49621.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0462, MT0478, lpdC / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.52 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2003
Details: Mirrors down stream of double crystal monochromator with sagitally focusing Si(111) crystal
RadiationMonochromator: sagitally focusing Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→19.94 Å / Num. all: 72840 / Num. obs: 72840 / % possible obs: 96.6 % / Observed criterion σ(I): -1 / Redundancy: 2.3 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.094 / Net I/σ(I): 9.3
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.8 / Num. unique all: 6930 / Rsym value: 0.464 / % possible all: 92.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 141899.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3396 4.9 %RANDOM
Rwork0.199 ---
all0.1991 ---
obs0.1991 69659 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4036 Å2 / ksol: 0.327908 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.97 Å20 Å20 Å2
2--10.52 Å20 Å2
3----6.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6938 0 106 341 7385
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 498 4.8 %
Rwork0.359 9982 -
obs--83.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fad_mpd.paramfad_xplor.top

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