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- PDB-3clu: Crystal structure of the R236K mutant from Methylophilus methylot... -

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Basic information

Entry
Database: PDB / ID: 3clu
TitleCrystal structure of the R236K mutant from Methylophilus methylotrophus ETF
Components
  • Electron transfer flavoprotein subunit alpha
  • Electron transfer flavoprotein subunit beta
KeywordsELECTRON TRANSPORT / ETF / TMADH / electron transfer / flavoprotein / dynamic interface / FAD / Transport
Function / homology
Function and homology information


fatty acid beta-oxidation using acyl-CoA dehydrogenase / 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 / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsKatona, G. / Leys, D.
CitationJournal: Biochemistry / Year: 2008
Title: Probing the dynamic interface between trimethylamine dehydrogenase (TMADH) and electron transferring flavoprotein (ETF) in the TMADH-2ETF complex: role of the Arg-alpha237 (ETF) and Tyr-442 (TMADH) residue pair.
Authors: Burgess, S.G. / Messiha, H.L. / Katona, G. / Rigby, S.E. / Leys, D. / Scrutton, N.S.
History
DepositionMar 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Electron transfer flavoprotein subunit beta
D: Electron transfer flavoprotein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7894
Polymers62,6562
Non-polymers1,1332
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-45.9 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.482, 116.482, 84.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Electron transfer flavoprotein subunit beta / Beta-ETF / Electron transfer flavoprotein small subunit / ETFSS


Mass: 28929.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophilus methylotrophus (bacteria)
Gene: etfB / Production host: Escherichia coli (E. coli) / References: UniProt: P53570
#2: Protein Electron transfer flavoprotein subunit alpha / Alpha-ETF / Electron transfer flavoprotein large subunit / ETFLS


Mass: 33726.125 Da / Num. of mol.: 1 / Mutation: R237K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophilus methylotrophus (bacteria)
Gene: etfA / Production host: Escherichia coli (E. coli) / References: UniProt: P53571
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growMethod: vapor diffusion / pH: 6.2
Details: limited digest with trypsin, 2.0 M sodium phosphate, pH 6.2, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→19 Å / Num. all: 58203 / Num. obs: 58203 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.067 / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1O97

1o97


Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.88 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20395 2793 5.1 %RANDOM
Rwork0.1678 ---
obs0.16963 52470 92.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.954 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.71 Å20 Å2
2--1.42 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 76 544 4833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224400
X-RAY DIFFRACTIONr_bond_other_d0.0010.024020
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9866003
X-RAY DIFFRACTIONr_angle_other_deg0.82539319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04625.371175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77615700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6071521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02808
X-RAY DIFFRACTIONr_nbd_refined0.2090.2922
X-RAY DIFFRACTIONr_nbd_other0.190.24303
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22265
X-RAY DIFFRACTIONr_nbtor_other0.0880.22544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2434
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.52923
X-RAY DIFFRACTIONr_mcbond_other0.21.51180
X-RAY DIFFRACTIONr_mcangle_it1.1924592
X-RAY DIFFRACTIONr_scbond_it1.96831699
X-RAY DIFFRACTIONr_scangle_it3.0374.51411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.804→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 205 -
Rwork0.252 3641 -
obs--87.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0541-0.134-0.21371.1153-0.07271.29970.00310.0096-0.0975-0.00280.01550.03620.15260.0226-0.0186-0.1836-0.0243-0.0236-0.1746-0.0088-0.118482.02544.7670.636
22.6412-0.7131-1.73010.41731.09042.86170.0790.4516-0.0143-0.1374-0.2591-0.108-0.214-0.69270.1801-0.13230.0876-0.01260.1670.016-0.10254.68763.78-22.348
31.37310.41760.30441.16540.35290.96580.04-0.17490.10180.2051-0.0310.1254-0.1394-0.0992-0.0089-0.1254-0.01540.029-0.1501-0.001-0.118873.62963.71913.859
42.0225-0.20880.18840.86780.35833.36370.11980.2420.0857-0.1018-0.1162-0.1268-0.2761-0.1488-0.0036-0.15450.04330.0221-0.0750.0277-0.081468.82664.583-18.389
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CA1 - 2361 - 236
2X-RAY DIFFRACTION2CA237 - 261237 - 261
3X-RAY DIFFRACTION3DB1 - 1942 - 195
4X-RAY DIFFRACTION4DB195 - 318196 - 319

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