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- PDB-1kfy: QUINOL-FUMARATE REDUCTASE WITH QUINOL INHIBITOR 2-[1-(4-CHLORO-PH... -

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Basic information

Entry
Database: PDB / ID: 1kfy
TitleQUINOL-FUMARATE REDUCTASE WITH QUINOL INHIBITOR 2-[1-(4-CHLORO-PHENYL)-ETHYL]-4,6-DINITRO-PHENOL
Components(FUMARATE REDUCTASE ...) x 4
KeywordsOXIDOREDUCTASE / fumarate reductase / succinate dehydrogenase / quinone / quinol / respiration / membrane protein
Function / homology
Function and homology information


plasma membrane fumarate reductase complex / fermentation / succinate dehydrogenase activity / anaerobic electron transport chain / fumarate metabolic process / : / succinate dehydrogenase / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...plasma membrane fumarate reductase complex / fermentation / succinate dehydrogenase activity / anaerobic electron transport chain / fumarate metabolic process / : / succinate dehydrogenase / 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 / 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 / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / 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 / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / 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. / 3 helical TM bundles of succinate and fumarate reductases / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / 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 / Rhinovirus 14, subunit 4 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 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 / FAD/NAD(P)-binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-[1-(4-CHLORO-PHENYL)-ETHYL]-4,6-DINITRO-PHENOL / O-DODECANYL OCTAETHYLENE GLYCOL / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / OXALOACETATE ION / 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 / ISOMORPHOUS REPLACEMENT / Resolution: 3.6 Å
AuthorsIverson, T.M. / Luna-Chavez, C. / Croal, L.R. / Cecchini, G. / Rees, D.C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site.
Authors: Iverson, T.M. / Luna-Chavez, C. / Croal, L.R. / Cecchini, G. / Rees, D.C.
#1: Journal: Science / Year: 1999
Title: Structure of the Escherichia coli Fumarate Reductase Respiratory Complex
Authors: Iverson, T.M. / Luna-Chavez, C. / Cecchini, G. / Rees, D.C.
History
DepositionNov 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUMARATE REDUCTASE FLAVOPROTEIN
B: Fumarate reductase iron-sulfur protein
C: FUMARATE REDUCTASE 15 KDA HYDROPHOBIC PROTEIN
D: FUMARATE REDUCTASE 13 KDA HYDROPHOBIC PROTEIN
M: FUMARATE REDUCTASE FLAVOPROTEIN
N: Fumarate reductase iron-sulfur protein
O: FUMARATE REDUCTASE 15 KDA HYDROPHOBIC PROTEIN
P: FUMARATE REDUCTASE 13 KDA HYDROPHOBIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,93623
Polymers242,1948
Non-polymers5,74115
Water0
1
A: FUMARATE REDUCTASE FLAVOPROTEIN
B: Fumarate reductase iron-sulfur protein
C: FUMARATE REDUCTASE 15 KDA HYDROPHOBIC PROTEIN
D: FUMARATE REDUCTASE 13 KDA HYDROPHOBIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,69811
Polymers121,0974
Non-polymers2,6017
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19080 Å2
ΔGint-176 kcal/mol
Surface area40120 Å2
MethodPISA
2
M: FUMARATE REDUCTASE FLAVOPROTEIN
N: Fumarate reductase iron-sulfur protein
O: FUMARATE REDUCTASE 15 KDA HYDROPHOBIC PROTEIN
P: FUMARATE REDUCTASE 13 KDA HYDROPHOBIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,23712
Polymers121,0974
Non-polymers3,1408
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18410 Å2
ΔGint-167 kcal/mol
Surface area40050 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.147, 137.814, 270.986
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


Mass: 66057.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PFA / Production host: Escherichia coli (E. coli) / References: UniProt: P00363, succinate dehydrogenase
#2: Protein Fumarate reductase iron-sulfur protein


Mass: 27021.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PFA / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC47, succinate dehydrogenase
#3: Protein 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 (E. coli) / Plasmid: PFA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q0
#4: Protein 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 (E. coli) / Plasmid: PFA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q3

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Non-polymers , 7 types, 15 molecules

#5: Chemical ChemComp-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


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


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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-BRS / 2-[1-(4-CHLORO-PHENYL)-ETHYL]-4,6-DINITRO-PHENOL / DNP-19


Mass: 322.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11ClN2O5
#11: Chemical ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT / Octaethylene glycol monododecyl ether


Mass: 538.755 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H58O9

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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: 3.7 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 5K MME, MgOAc, EDTA, Na Citrate, DTT, DNP-19, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
20.7 %(w/v)polyoxyethylene getergent C12E91drop
312.5 %PEG5000 MME1reservoir
485 mMmagnesium acetate1reservoir
5100 mMsodium citrate1reservoirpH5.8
60.100 mMEDTA1reservoir
70.001 %dithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 38919 / Num. obs: 38919 / % possible obs: 91.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rsym value: 0.104 / Net I/σ(I): 12
Reflection shellResolution: 3.6→3.66 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.301 / % possible all: 90.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 124660 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 90.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 1KF6

1kf6


Resolution: 3.6→50 Å / σ(F): 0 / Details: REFMAC WAS ALSO USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.301 819 2.1 %RANDOM
Rwork0.264 ---
all-38919 --
obs-38919 --
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16640 0 317 0 16957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0165
X-RAY DIFFRACTIONc_angle_deg1.9
Refinement
*PLUS
Highest resolution: 3.6 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 2.1 % / Rfactor obs: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0165

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