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- PDB-3clr: Crystal structure of the R236A ETF mutant from M. methylotrophus -

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Basic information

Entry
Database: PDB / ID: 3clr
TitleCrystal structure of the R236A ETF mutant from M. methylotrophus
Components(Electron transfer flavoprotein subunit ...) x 2
KeywordsELECTRON TRANSPORT / ETF / TMADH / electron transfer / flavoprotein / 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 / PHOSPHATE ION / Electron transfer flavoprotein subunit beta / Electron transfer flavoprotein subunit alpha
Similarity search - Component
Biological speciesMethylophilus methylotrophus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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

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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)63,8265
Polymers62,5982
Non-polymers1,2283
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-48.2 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.009, 117.009, 84.513
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Electron transfer flavoprotein subunit ... , 2 types, 2 molecules CD

#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: 33668.023 Da / Num. of mol.: 1 / Mutation: R237A
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

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Non-polymers , 4 types, 734 molecules

#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.2
Details: limited digest with trypsin, 2.0 M sodium phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP

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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: 1.9→20 Å / Num. all: 49299 / Num. obs: 49299 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.074 / Net I/σ(I): 8.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1O97

1o97


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.411 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18169 2610 5 %RANDOM
Rwork0.14775 ---
obs0.14947 49299 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 81 731 5064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224481
X-RAY DIFFRACTIONr_bond_other_d0.0020.024095
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9886112
X-RAY DIFFRACTIONr_angle_other_deg0.84239516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.385588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99625.363179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96315732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3141522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02822
X-RAY DIFFRACTIONr_nbd_refined0.2160.2900
X-RAY DIFFRACTIONr_nbd_other0.1880.24312
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22255
X-RAY DIFFRACTIONr_nbtor_other0.0880.22509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2563
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6950.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9331.53083
X-RAY DIFFRACTIONr_mcbond_other0.2341.51192
X-RAY DIFFRACTIONr_mcangle_it1.25324659
X-RAY DIFFRACTIONr_scbond_it2.23231768
X-RAY DIFFRACTIONr_scangle_it3.3494.51453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 185 -
Rwork0.168 3497 -
obs--97.07 %
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)
10.7801-0.1068-0.19790.77070.14840.81650.0039-0.0032-0.07730.00450.01850.01120.09240.0468-0.0224-0.1389-0.0181-0.0177-0.129-0.0061-0.117482.39245.0110.642
21.8121-0.7413-1.54060.7731.19011.97710.13660.25260.011-0.1362-0.2476-0.0469-0.3028-0.58990.1111-0.09290.0955-0.00810.06010.0172-0.109854.89964.045-22.418
31.16150.41210.25560.76870.31750.76170.0374-0.11710.09850.0699-0.0330.0685-0.0863-0.0566-0.0044-0.1342-0.00830.0141-0.1306-0.0042-0.127373.90764.02813.896
41.43670.1011-0.13621.01240.19663.09140.12320.12850.0932-0.0958-0.111-0.0887-0.3148-0.0043-0.0122-0.10630.03920.0224-0.06560.0215-0.106469.0164.924-18.52
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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