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- PDB-1o94: Ternary complex between trimethylamine dehydrogenase and electron... -

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Basic information

Entry
Database: PDB / ID: 1o94
TitleTernary complex between trimethylamine dehydrogenase and electron transferring flavoprotein
Components
  • (ELECTRON TRANSFER FLAVOPROTEIN ...) x 2
  • TRIMETHYLAMINE DEHYDROGENASE
KeywordsELECTRON TRANSPORT / PROTEIN COMPLEX / ELECTRON TRANSFER / DEHYDROGENASE
Function / homology
Function and homology information


trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / catabolic process / FMN binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding
Similarity search - Function
Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / : / OYE-like second alpha/beta domain / : / 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 ...Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / : / OYE-like second alpha/beta domain / : / 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 / NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / DHS-like NAD/FAD-binding domain superfamily / Pyridine nucleotide-disulphide oxidoreductase / HUPs / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Rossmann-like alpha/beta/alpha sandwich fold / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / Trimethylamine dehydrogenase / Electron transfer flavoprotein subunit beta / Electron transfer flavoprotein subunit alpha
Similarity search - Component
Biological speciesMETHYLOPHILUS METHYLOTROPHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Sep 18, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIMETHYLAMINE DEHYDROGENASE
B: TRIMETHYLAMINE DEHYDROGENASE
C: ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT
D: ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT
E: ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT
F: ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,48214
Polymers288,3186
Non-polymers3,1658
Water38,7142149
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25990 Å2
ΔGint-102.8 kcal/mol
Surface area93580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)118.930, 211.543, 125.970
Angle α, β, γ (deg.)90.00, 100.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2310-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TRIMETHYLAMINE DEHYDROGENASE / TMADH


Mass: 81606.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: LINK BETWEEN FMN AND RESIDUE 30 / Source: (natural) METHYLOPHILUS METHYLOTROPHUS (bacteria) / References: UniProt: P16099, EC: 1.5.99.7

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ELECTRON TRANSFER FLAVOPROTEIN ... , 2 types, 4 molecules CEDF

#2: Protein ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT


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


Mass: 33622.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53571

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Non-polymers , 5 types, 2157 molecules

#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 2149 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growpH: 6.5
Details: 8% PEG 20000, 8% PEG 750 MME, 0.1-0.3 M SODIUM ACETATE, pH 6.50
Crystal grow
*PLUS
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: SRS / Beamline: PX9.6 / Wavelength: 1
DetectorDetector: CCD / Date: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 184949 / % possible obs: 94.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.9 / % possible all: 89.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 184250 / Num. measured all: 1099561
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 89.5 %

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TMD

2tmd


Resolution: 2→19.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.369 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: DISORDERED REGIONS ARE NOT INCLUDED IN THE COORDINATES. THE ENTIRE FAD DOMAIN OF THE ETF MOLECULES IS NOT VISIBLE IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 9811 5 %RANDOM
Rwork0.172 ---
obs0.174 184949 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: 33.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å2-0.65 Å2
2---1.76 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17598 0 178 2149 19925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02118174
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.9751.95924740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98852297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39924799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.579152870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.27315119
X-RAY DIFFRACTIONr_chiral_restr0.1440.22719
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213897
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.28885
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.21870
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3770.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0171.511432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.749218330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.15336742
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8444.56386
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 689
Rwork0.238 12462
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.01

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