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- PDB-2eq7: Crystal structure of lipoamide dehydrogenase from thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 2eq7
TitleCrystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdo
Components
  • 2-oxoglutarate dehydrogenase E2 component
  • 2-oxoglutarate dehydrogenase E3 component
KeywordsOXIDOREDUCTASE / PROTEIN-PROTEIN COMPLEX / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / pyruvate metabolic process / tricarboxylic acid cycle / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
: / Dihydrolipoamide succinyltransferase / : / Dihydrolipoamide dehydrogenase / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. ...: / Dihydrolipoamide succinyltransferase / : / Dihydrolipoamide dehydrogenase / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / FAD/NAD-linked reductase, dimerisation domain superfamily / Chloramphenicol acetyltransferase-like 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakai, T. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of lipoamide dehydrogenase from Thermus thermophilus HB8
Authors: Nakai, T. / Kamiya, N.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-oxoglutarate dehydrogenase E3 component
B: 2-oxoglutarate dehydrogenase E3 component
C: 2-oxoglutarate dehydrogenase E2 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5077
Polymers102,6103
Non-polymers2,8984
Water20,8791159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-61.5 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.028, 107.073, 131.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2-oxoglutarate dehydrogenase E3 component / Lipoamide dehydrogenase / Dihydrolipoamide dehydrogenase


Mass: 49127.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0287 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: Q5SLK6, dihydrolipoyl dehydrogenase
#2: Protein/peptide 2-oxoglutarate dehydrogenase E2 component / Dihydrolipoamide succinyltransferase


Mass: 4354.039 Da / Num. of mol.: 1 / Fragment: peripheral subunit binding domain / Source method: obtained synthetically
Details: The 40-residue peptide corresponding to a domain of the TTHA0288 protein was synthesized by Greiner
References: UniProt: Q5SLK5, dihydrolipoyllysine-residue succinyltransferase
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 1159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 45%(v/v) MPD, 200mM NaCl, 10mM NAD+, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 111571 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 25.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.6 / Num. unique all: 10985 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EQ6

2eq6


Resolution: 1.8→39.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2723055.64 / 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
Rfree0.238 5581 5 %RANDOM
Rwork0.207 ---
obs0.207 111470 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.0469 Å2 / ksol: 0.345653 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å20 Å2
2---1.92 Å20 Å2
3---5.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7130 0 194 1159 8483
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 956 5.2 %
Rwork0.247 17320 -
obs-18276 99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3FAD.param
X-RAY DIFFRACTION4NAD.param

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