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- PDB-2eq9: Crystal structure of lipoamide dehydrogenase from thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 2eq9
TitleCrystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb
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 / lipoic acid binding / 2-oxoglutarate metabolic process / pyruvate metabolic process / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
E3-binding domain / Dihydrolipoamide Transferase / : / 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 ...E3-binding domain / Dihydrolipoamide Transferase / : / 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 / Few Secondary Structures / Irregular / 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: 2.09 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_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
Revision 1.3Oct 30, 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
G: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
H: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
I: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
J: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
K: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
L: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,30020
Polymers411,01512
Non-polymers6,2848
Water18,1411007
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)104,3255
Polymers102,7543
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)104,3255
Polymers102,7543
Non-polymers1,5712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
H: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
I: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3255
Polymers102,7543
Non-polymers1,5712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
K: Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
L: Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3255
Polymers102,7543
Non-polymers1,5712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.781, 88.877, 144.149
Angle α, β, γ (deg.)89.26, 87.01, 70.84
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 49151.836 Da / Num. of mol.: 8
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


Mass: 4450.195 Da / Num. of mol.: 4 / Fragment: Peripheral subunit binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0232 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)
References: UniProt: Q5SLR1, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30%(w/v) PEG MME 5000, 200mM ammonium sulfate, 100mM MES, pH 6.5, 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 JUPITER 210 / Detector: CCD / Date: Mar 8, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 238181 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.3
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 1.7 / Num. unique all: 21564 / % possible all: 87.4

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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: 2.09→43.62 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2304764.35 / 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
Rfree0.257 11946 5 %RANDOM
Rwork0.217 ---
obs0.217 238176 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6929 Å2 / ksol: 0.335389 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-7.08 Å2-2.87 Å2
2---0.26 Å2-0.44 Å2
3---0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.09→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28396 0 424 1007 29827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 1801 4.9 %
Rwork0.281 35153 -
obs-36954 89.9 %
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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