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- PDB-5vpn: E. coli Quinol fumarate reductase FrdA E245Q mutation -

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Basic information

Entry
Database: PDB / ID: 5vpn
TitleE. coli Quinol fumarate reductase FrdA E245Q mutation
Components
  • (Fumarate reductase subunit ...) x 2
  • Fumarate reductase flavoprotein subunit
  • Succinate dehydrogenase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / quinol fumarate reductase / fumarate reduction / membrane protein / Complex II Superfamily
Function / homology
Function and homology information


: / : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding ...: / : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / bacterial-type flagellum assembly / tricarboxylic acid cycle / FAD binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA damage response / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA ...Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / 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 / Alpha-helical ferredoxin / FAD binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Fumarate reductase iron-sulfur subunit / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C / Fumarate reductase subunit D / Fumarate reductase iron-sulfur subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2232 Å
AuthorsStarbird, C.A. / Maklashina, E. / Sharma, P. / Qualls-Histed, S. / Cecchini, G. / Iverson, T.M.
Funding support United States, 6items
OrganizationGrant numberCountry
Department of Veterans AffairsBX001077 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061606 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008320 United States
National Science Foundation (NSF, United States)DGE:0909667 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105404 United States
High-End Instrumentation GrantS10OD018483 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase.
Authors: Starbird, C.A. / Maklashina, E. / Sharma, P. / Qualls-Histed, S. / Cecchini, G. / Iverson, T.M.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_initial_refinement_model / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession

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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: Succinate dehydrogenase iron-sulfur subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
E: Fumarate reductase flavoprotein subunit
F: Succinate dehydrogenase iron-sulfur subunit
G: Fumarate reductase subunit C
H: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,97616
Polymers238,7588
Non-polymers3,2188
Water00
1
A: Fumarate reductase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9888
Polymers119,3794
Non-polymers1,6094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17140 Å2
ΔGint-159 kcal/mol
Surface area39780 Å2
MethodPISA
2
E: Fumarate reductase flavoprotein subunit
F: Succinate dehydrogenase iron-sulfur subunit
G: Fumarate reductase subunit C
H: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9888
Polymers119,3794
Non-polymers1,6094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16960 Å2
ΔGint-157 kcal/mol
Surface area40130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.565, 138.134, 220.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein Fumarate reductase flavoprotein subunit


Mass: 64339.711 Da / Num. of mol.: 2 / Mutation: E245Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: frdA, b4154, JW4115 / Production host: Escherichia coli (E. coli) / References: UniProt: P00363, fumarate reductase (quinol)
#2: Protein Succinate dehydrogenase iron-sulfur subunit


Mass: 27021.885 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: A0A076YHN1, UniProt: P0AC49*PLUS, succinate dehydrogenase

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Fumarate reductase subunit ... , 2 types, 4 molecules CGDH

#3: Protein Fumarate reductase subunit C / Fumarate reductase 15 kDa hydrophobic protein


Mass: 14898.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: frdC, b4152, JW4113 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q0
#4: Protein Fumarate reductase subunit D / Fumarate reductase 13 kDa hydrophobic protein


Mass: 13118.870 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: frdD, b4151, JW4112 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q3

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Non-polymers , 4 types, 8 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#8: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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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: 4.25 Å3/Da / Density % sol: 71.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals of the QFR-FrdAE245Q mutant were grown using the hanging-drop vapor diffusion method in droplets containing protein solution (15 mg/ml QFR FrdAE245Q in 25 mM Tris-HCl pH 7.4, 1 mM ...Details: Crystals of the QFR-FrdAE245Q mutant were grown using the hanging-drop vapor diffusion method in droplets containing protein solution (15 mg/ml QFR FrdAE245Q in 25 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.02 % C12E9) and the reservoir solution (275 mM NaMalonate, 19% polyethylene glycol 6000, 100 mM NaCitrate pH 4.0, 1 mM EDTA and 0.001% dithiothreitol) in a 1:1 ratio.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 4.22→50 Å / Num. obs: 28494 / % possible obs: 96.8 % / Redundancy: 5.5 % / Net I/σ(I): 1.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L0V

1l0v


Resolution: 4.2232→22.962 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.59
RfactorNum. reflection% reflection
Rfree0.2704 1417 4.97 %
Rwork0.2148 --
obs0.2176 28494 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 469.59 Å2 / Biso mean: 214.5661 Å2 / Biso min: 67.98 Å2
Refinement stepCycle: final / Resolution: 4.2232→22.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16701 0 144 0 16845
Biso mean--219.38 --
Num. residues----2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317270
X-RAY DIFFRACTIONf_angle_d0.61423468
X-RAY DIFFRACTIONf_chiral_restr0.0422563
X-RAY DIFFRACTIONf_plane_restr0.0053005
X-RAY DIFFRACTIONf_dihedral_angle_d15.84210150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2232-4.37310.41761350.34132580271593
4.3731-4.54690.38531460.31472704285097
4.5469-4.75210.38451270.29132659278696
4.7521-5.00020.28991410.27462602274393
5.0002-5.30990.32951380.2392509264789
5.3099-5.7140.31351410.22422725286698
5.714-6.27830.24681490.217828112960100
6.2783-7.16260.27471510.205728262977100
7.1626-8.93480.21781470.17022840298799
8.9348-22.96260.20891420.16292821296395
Refinement TLS params.Method: refined / Origin x: -3.395 Å / Origin y: -38.8332 Å / Origin z: 6.8835 Å
111213212223313233
T1.3899 Å20.0541 Å2-0.0667 Å2-1.0052 Å2-0.0241 Å2--1.0079 Å2
L0.5117 °2-0.0149 °20.0147 °2-0.1407 °2-0.0913 °2--0.3038 °2
S0.0936 Å °0.1819 Å °0.0031 Å °-0.5347 Å °-0.0628 Å °0.0863 Å °-0.1879 Å °-0.0028 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 576
2X-RAY DIFFRACTION1allA703
3X-RAY DIFFRACTION1allB1 - 243
4X-RAY DIFFRACTION1allB244 - 246
5X-RAY DIFFRACTION1allC1 - 130
6X-RAY DIFFRACTION1allD0 - 118
7X-RAY DIFFRACTION1allE0 - 584
8X-RAY DIFFRACTION1allE703
9X-RAY DIFFRACTION1allF1 - 243
10X-RAY DIFFRACTION1allF244 - 246
11X-RAY DIFFRACTION1allG1 - 130
12X-RAY DIFFRACTION1allH0 - 118

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