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- PDB-1o96: Structure of electron transferring flavoprotein for Methylophilus... -

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Basic information

Entry
Database: PDB / ID: 1o96
TitleStructure of electron transferring flavoprotein for Methylophilus methylotrophus.
Components
  • ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
  • ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
KeywordsELECTRON TRANSFER / FLAVOPROTEIN / FAD BINDING
Function / homology
Function and homology information


flavin adenine dinucleotide binding / electron transfer activity / nucleotide binding
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 beta / Electron transfer flavoprotein subunit alpha
Similarity search - Component
Biological speciesMETHYLOPHILUS METHYLOTROPHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLeys, D. / Basran, J. / Talfournier, F. / Sutcliffe, M.J. / Scrutton, N.S.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Extensive Conformational Sampling in a Ternary Electron Transfer Complex.
Authors: Leys, D. / Basran, J. / Talfournier, F. / Sutcliffe, M.J. / Scrutton, N.S.
History
DepositionDec 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
B: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
C: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
D: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
E: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
F: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
Q: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
Z: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,74216
Polymers250,2118
Non-polymers4,5318
Water00
1
A: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
B: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6864
Polymers62,5532
Non-polymers1,1332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
D: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6864
Polymers62,5532
Non-polymers1,1332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
F: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6864
Polymers62,5532
Non-polymers1,1332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
Q: ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT
Z: ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6864
Polymers62,5532
Non-polymers1,1332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.516, 126.877, 221.390
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
ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT / BETA-ETF / ELECTRON TRANSFER FLAVOPROTEIN SMALL SUBUNIT / ETFSS


Mass: 28929.850 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53570
#2: Protein
ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT / ALPHA-ETF / ELECTRON TRANSFER FLAVOPROTEIN LARGE SUBUNIT / ETFLS


Mass: 33622.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53571
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Sequence detailsDISORDERED REGIONS WERE NOT INCORPORATED IN THE MODEL. THE FAD DOMAIN OF ETF Q-Z IS MODELLED WITH ...DISORDERED REGIONS WERE NOT INCORPORATED IN THE MODEL. THE FAD DOMAIN OF ETF Q-Z IS MODELLED WITH OCCUPANCY 0.5 DUE TO ITS HIGH MOBILITY.

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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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growpH: 9 / Details: SATURATED SODIUM CITRATE, pH 9.00
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG200001reservoir
20.2 Msodium acetate1reservoir
30.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorDetector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 58411 / % possible obs: 98.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.5
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 553173
Reflection shell
*PLUS
Lowest resolution: 3.21 Å / % possible obs: 98.5 %

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.92 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.874 / SU B: 20.23 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: DISORDERED REGIONS WERE NOT INCORPORATED IN THE MODEL. THE FAD DOMAIN OF ETF Q-Z IS MODELLED WITH OCCUPANCY 0.5 DUE TO ITS HIGH MOBILITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2989 5.1 %RANDOM
Rwork0.212 ---
obs0.215 56199 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.11 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å20 Å2
2--4.75 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16789 0 304 0 17093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02117354
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8131.98223626
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.93352264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3624.971678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.045152747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9561593
X-RAY DIFFRACTIONr_chiral_restr0.1640.22799
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212901
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2780.27625
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2560
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2191.511288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.376218069
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.30636066
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.0784.55557
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 208
Rwork0.255 4041
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.034
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.94

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