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- PDB-1efv: THREE-DIMENSIONAL STRUCTURE OF HUMAN ELECTRON TRANSFER FLAVOPROTE... -

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Basic information

Entry
Database: PDB / ID: 1efv
TitleTHREE-DIMENSIONAL STRUCTURE OF HUMAN ELECTRON TRANSFER FLAVOPROTEIN TO 2.1 A RESOLUTION
Components(ELECTRON TRANSFER FLAVOPROTEIN) x 2
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN / GLUTARIC ACIDEMIA TYPE II
Function / homology
Function and homology information


electron transfer flavoprotein complex / fatty acid beta-oxidation using acyl-CoA dehydrogenase / Respiratory electron transport / amino acid catabolic process / Protein methylation / respiratory electron transport chain / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer activity / mitochondrial matrix / mitochondrion
Similarity search - Function
Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein domain / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal ...Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein domain / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain / Electron transfer flavoprotein domain / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Electron transfer flavoprotein subunit alpha, mitochondrial / Electron transfer flavoprotein subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsRoberts, D.L. / Frerman, F.E. / Kim, J.J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Three-dimensional structure of human electron transfer flavoprotein to 2.1-A resolution.
Authors: Roberts, D.L. / Frerman, F.E. / Kim, J.J.
History
DepositionOct 16, 1996Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELECTRON TRANSFER FLAVOPROTEIN
B: ELECTRON TRANSFER FLAVOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1534
Polymers61,0202
Non-polymers1,1332
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-41 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.437, 103.872, 63.696
Angle α, β, γ (deg.)90.00, 109.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ELECTRON TRANSFER FLAVOPROTEIN / ETF / HETF / ELECTRON TRANSFERRING FLAVOPROTEIN


Mass: 33134.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COFACTORS FAD 1 AND AMP 1 ARE NON-COVALENTLY BOUND / Source: (gene. exp.) Homo sapiens (human) / Cellular location: MITOCHONDRIA / Organ: LIVER / Plasmid: PBLUESCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P13804
#2: Protein ELECTRON TRANSFER FLAVOPROTEIN / ETF / HETF / ELECTRON TRANSFERRING FLAVOPROTEIN


Mass: 27885.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COFACTORS FAD 1 AND AMP 1 ARE NON-COVALENTLY BOUND / Source: (gene. exp.) Homo sapiens (human) / Cellular location: MITOCHONDRIA / Organ: LIVER / Plasmid: PBLUESCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P38117
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.69 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: THE PROTEIN WAS CRYSTALLIZED FROM 15 % PEG 1500, 50 MM HEPES, PH 7.0. EQUAL VOLUMES OF PROTEIN (15 MG/ML) AND PRECIPITANT WERE MIXED IN SITTING DROPS., vapor diffusion - sitting drop
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
215 %PEG15001drop
350 mMHEPES1drop
415 %PEG15001reservoir
550 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 32383 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 17
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.304 / % possible all: 92.4
Reflection
*PLUS
% possible obs: 95.6 % / Num. measured all: 118435
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.304

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Processing

Software
NameVersionClassification
HEAVYmodel building
PHASESphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
HEAVYphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2794 10 %RANDOM
Rwork0.172 ---
obs0.172 27942 90.41 %-
Displacement parametersBiso mean: 27.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 76 258 4559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.223 272 7.878 %
Rwork0.218 2484 -
obs--80.03 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDXJ.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171 / Rfactor Rfree: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18
LS refinement shell
*PLUS
Rfactor obs: 0.218

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