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- PDB-6b58: FrdA-SdhE assembly intermediate -

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Basic information

Entry
Database: PDB / ID: 6b58
TitleFrdA-SdhE assembly intermediate
Components
  • FAD assembly factor SdhE
  • Fumarate reductase flavoprotein subunit
KeywordsFLAVOPROTEIN / FrdA / assembly intermediate / complex / respiration
Function / homology
Function and homology information


respiratory chain complex II assembly / : / succinate metabolic process / fermentation / succinate dehydrogenase activity / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / bacterial-type flagellum assembly ...respiratory chain complex II assembly / : / succinate metabolic process / fermentation / succinate dehydrogenase activity / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / bacterial-type flagellum assembly / FAD binding / flavin adenine dinucleotide binding / electron transfer activity / DNA damage response / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / Fumarate reductase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA ...: / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / Fumarate reductase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / : / MALONATE ION / DI(HYDROXYETHYL)ETHER / Fumarate reductase flavoprotein subunit / FAD assembly factor SdhE / FAD assembly factor SdhE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.611 Å
AuthorsSharma, P. / Iverson, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061606 United States
Department of Veterans AffairsBX001077 United States
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of an assembly intermediate of respiratory Complex II.
Authors: Sharma, P. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
History
DepositionSep 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarate reductase flavoprotein subunit
B: FAD assembly factor SdhE
C: Fumarate reductase flavoprotein subunit
D: FAD assembly factor SdhE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,18126
Polymers146,3344
Non-polymers2,84722
Water1,13563
1
A: Fumarate reductase flavoprotein subunit
B: FAD assembly factor SdhE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,65315
Polymers73,1672
Non-polymers1,48613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-11 kcal/mol
Surface area23760 Å2
MethodPISA
2
C: Fumarate reductase flavoprotein subunit
D: FAD assembly factor SdhE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,52811
Polymers73,1672
Non-polymers1,3619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-17 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.640, 63.330, 175.580
Angle α, β, γ (deg.)90.00, 96.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Fumarate reductase flavoprotein subunit


Mass: 63477.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00363, fumarate reductase (quinol)
#2: Protein FAD assembly factor SdhE


Mass: 9689.108 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P64561, UniProt: P64559*PLUS

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Non-polymers , 8 types, 85 molecules

#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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 90 mM Bis-Tris pH 5.5, 100 mM NH4CH3COO, 20% PEG 10,000 and 50mM NaMalonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 41620 / % possible obs: 96.8 % / Redundancy: 5 % / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF6

1kf6


Resolution: 2.611→37.153 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2025 4.87 %
Rwork0.1914 --
obs0.1946 41598 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.611→37.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9308 0 188 63 9559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019677
X-RAY DIFFRACTIONf_angle_d1.06813105
X-RAY DIFFRACTIONf_dihedral_angle_d6.1336594
X-RAY DIFFRACTIONf_chiral_restr0.0571430
X-RAY DIFFRACTIONf_plane_restr0.0071730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6113-2.67660.29841230.25492561X-RAY DIFFRACTION88
2.6766-2.74890.34851490.27262825X-RAY DIFFRACTION97
2.7489-2.82980.41661500.27422823X-RAY DIFFRACTION97
2.8298-2.92110.35271130.26232875X-RAY DIFFRACTION97
2.9211-3.02550.34141410.23262872X-RAY DIFFRACTION98
3.0255-3.14650.29871360.2222857X-RAY DIFFRACTION98
3.1465-3.28970.31581510.22152845X-RAY DIFFRACTION97
3.2897-3.4630.26081630.20512588X-RAY DIFFRACTION89
3.463-3.67980.27071370.17572845X-RAY DIFFRACTION97
3.6798-3.96360.20411440.16792927X-RAY DIFFRACTION99
3.9636-4.36190.23211600.162893X-RAY DIFFRACTION99
4.3619-4.99180.2181750.15732892X-RAY DIFFRACTION98
4.9918-6.28420.23531500.19052880X-RAY DIFFRACTION97
6.2842-37.15680.21211330.17512890X-RAY DIFFRACTION94

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