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- PDB-1efp: ELECTRON TRANSFER FLAVOPROTEIN (ETF) FROM PARACOCCUS DENITRIFICANS -

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Basic information

Entry
Database: PDB / ID: 1efp
TitleELECTRON TRANSFER FLAVOPROTEIN (ETF) FROM PARACOCCUS DENITRIFICANS
Components(PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)) x 2
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN / GLUTARIC ACIDEMIA TYPE II
Function / homology
Function and homology information


flavin adenine dinucleotide binding / electron transfer activity
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 / Electron transfer flavoprotein subunit beta
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRoberts, D.L. / Salazar, D. / Fulmer, J.P. / Frerman, F.E. / Kim, J.J.-P.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal structure of Paracoccus denitrificans electron transfer flavoprotein: structural and electrostatic analysis of a conserved flavin binding domain.
Authors: Roberts, D.L. / Salazar, D. / Fulmer, J.P. / Frerman, F.E. / Kim, J.J.
#1: Journal: 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.
#2: Journal: Protein Sci. / Year: 1995
Title: Crystallization and Preliminary X-Ray Analysis of Electron Transfer Flavoproteins from Human and Paracoccus Denitrificans
Authors: Roberts, D.L. / Herrick, K.R. / Frerman, F.E. / Kim, J.J.
History
DepositionDec 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
B: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
C: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
D: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0648
Polymers115,7994
Non-polymers2,2664
Water1,820101
1
A: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
B: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0324
Polymers57,8992
Non-polymers1,1332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-38 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
D: PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0324
Polymers57,8992
Non-polymers1,1332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-40 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.430, 80.530, 183.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.987, -0.161, 0.009), (-0.159, 0.982, 0.1), (-0.025, 0.098, -0.995)
Vector: 68.693, -1.56, 133.502)

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Components

#1: Protein PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN) / ETF


Mass: 31192.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FAD AND AMP COFACTORS ARE NONCOVALENTLY BOUND / Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Plasmid: BLUESCRIPT / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P38974
#2: Protein PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN) / ETF


Mass: 26707.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FAD AND AMP COFACTORS ARE NONCOVALENTLY BOUND / Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Plasmid: BLUESCRIPT / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P38975
#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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.33 Å3/Da / Density % sol: 49 %
Crystal growpH: 5.8
Details: 18% PEG 8000, 25 MM KH2PO4, 100 UM FAD, AND 5 MM MGCL2, FINAL PH = 5.8. THE PROTEIN WAS MIXED WITH SOLUTION IN A 1:1 RATIO (PROTEIN WAS IN 10 MM TRIS, PH 7.4).
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
218 %(w/v)PEG80001reservoir
325 mMpotassium phosphate1reservoir
40.100 mMFAD1reservoir
55 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 28666 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054
Reflection
*PLUS
Num. measured all: 118452

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EFV

1efv


Resolution: 2.6→12 Å / Rfactor Rfree error: 0.0061 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2197 7.5 %RANDOM
Rwork0.193 ---
obs0.193 28666 87.8 %-
Displacement parametersBiso mean: 26.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8038 0 152 101 8291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.75
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.242
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: 2.6→2.75 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3395 147 8.3 %
Rwork0.259 1624 -
obs--51.6 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / σ(F): 3 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.75
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.242
LS refinement shell
*PLUS
% reflection Rfree: 8.3 % / Rfactor Rwork: 0.259

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