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- PDB-2eq8: Crystal structure of lipoamide dehydrogenase from thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 2eq8
TitleCrystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp
Components
  • Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
  • Pyruvate dehydrogenase complex, dihydrolipoamide 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 / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / pyruvate decarboxylation to acetyl-CoA / 2-oxoglutarate metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
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 ...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 / 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 / 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 / Dihydrolipoyl dehydrogenase / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
B: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
C: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
D: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
E: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
F: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,33510
Polymers205,1936
Non-polymers3,1424
Water34,0301889
1
A: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
B: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
C: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1685
Polymers102,5973
Non-polymers1,5712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
E: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
F: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1685
Polymers102,5973
Non-polymers1,5712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.758, 104.082, 112.856
Angle α, β, γ (deg.)90.00, 107.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component / Lipoamide dehydrogenase


Mass: 49151.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0233 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: Q5SLR0, dihydrolipoyl dehydrogenase
#2: Protein/peptide Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component / Pyruvate dehydrogenase e2 component


Mass: 4292.950 Da / Num. of mol.: 2 / Fragment: Peripheral subunit binding domain / Source method: obtained synthetically
Details: The 40-residue peptide corresponding to a domain of the TTHA0184 protein was synthesized by Greiner
References: UniProt: Q5SLV9, dihydrolipoyllysine-residue acetyltransferase
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1889 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14%(w/v) PEG 3350, 100mM HEPES, 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: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 28, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 139010 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 39.1
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 10.2 / Num. unique all: 13440 / % possible all: 96.3

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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: 1.94→46.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2706511.34 / 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
Rfree0.244 6979 5 %RANDOM
Rwork0.207 ---
obs0.207 138941 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3615 Å2 / ksol: 0.301858 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--10.4 Å20 Å2-0.05 Å2
2--5.84 Å20 Å2
3---4.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.94→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14226 0 212 1889 16327
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_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 1155 5 %
Rwork0.24 21893 -
obs-23048 99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3FAD.param

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