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- PDB-3cir: E. coli Quinol fumarate reductase FrdA T234A mutation -

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Basic information

Entry
Database: PDB / ID: 3cir
TitleE. coli Quinol fumarate reductase FrdA T234A mutation
Components(Fumarate reductase ...) x 4
KeywordsOXIDOREDUCTASE / electron transport / Tricarboxylic acid cycle
Function / homology
Function and homology information


fumarate reductase complex / fermentation / succinate dehydrogenase activity / fumarate metabolic process / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...fumarate reductase complex / fermentation / succinate dehydrogenase activity / fumarate metabolic process / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-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 / metal ion binding / membrane / 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 / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain ...Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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 / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / 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 / Rhinovirus 14, subunit 4 / FAD binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / FAD/NAD(P)-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / FAD/NAD(P)-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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / 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: 3.65 Å
AuthorsTomasiak, T.M. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II.
Authors: Tomasiak, T.M. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 28, 2021Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs ..._refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 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
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur subunit
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,35216
Polymers242,1348
Non-polymers3,2188
Water00
1
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6768
Polymers121,0674
Non-polymers1,6094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40140 Å2
ΔGint-152.9 kcal/mol
Surface area16910 Å2
MethodPISA
2
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur subunit
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6768
Polymers121,0674
Non-polymers1,6094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40000 Å2
ΔGint-145.9 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.861, 135.468, 266.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Fumarate reductase ... , 4 types, 8 molecules AMBNCODP

#1: Protein Fumarate reductase flavoprotein subunit / E.C.1.3.99.1


Mass: 66027.523 Da / Num. of mol.: 2 / Mutation: T234A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FrdA / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P00363, EC: 1.3.99.1
#2: Protein Fumarate reductase iron-sulfur subunit / E.C.1.3.99.1


Mass: 27021.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FrdB / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0AC47, EC: 1.3.99.1
#3: Protein Fumarate reductase subunit C / E.C.1.3.99.1


Mass: 14898.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FrdC / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0A8Q0, EC: 1.3.99.1
#4: Protein Fumarate reductase subunit D / E.C.1.3.99.1


Mass: 13118.870 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FrdD / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0A8Q3, EC: 1.3.99.1

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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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 10% PEG 5000 MME, 0.250M magnesium acetate, 100mM citric acid, 0.001M EDTA, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.65→266 Å / Num. all: 40327 / Num. obs: 32532 / % possible obs: 80.7 % / Observed criterion σ(F): -3 / Rsym value: 0.39
Reflection shellResolution: 3.65→3.71 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.391 / % possible all: 55.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B76

2b76


Resolution: 3.65→266 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 621 2 %Random
Rwork0.2605 ---
all-39759 --
obs-32130 80.8 %-
Refinement stepCycle: LAST / Resolution: 3.65→266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15602 0 144 0 15746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011442
X-RAY DIFFRACTIONc_angle_deg1.91299
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.65→3.76 Å
RfactorNum. reflection
Rfree0.4117 37
Rwork0.3784 -
obs-1831

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