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- PDB-1kf6: E. coli Quinol-Fumarate Reductase with Bound Inhibitor HQNO -

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Basic information

Entry
Database: PDB / ID: 1kf6
TitleE. coli Quinol-Fumarate Reductase with Bound Inhibitor HQNO
Components(FUMARATE REDUCTASE ...) x 4
KeywordsOXIDOREDUCTASE / respiration / fumarate reductace / succinate dehydrogenase / complex II / quinol / quinone
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 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / FAD/NAD(P)-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / 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
ACETATE ION / O-DODECANYL OCTAETHYLENE GLYCOL / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / : / OXALOACETATE ION / IRON/SULFUR CLUSTER / Fumarate reductase flavoprotein subunit ...ACETATE ION / O-DODECANYL OCTAETHYLENE GLYCOL / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / : / 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 / Resolution: 2.7 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 19, 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_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.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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_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)249,38031
Polymers242,1948
Non-polymers7,18623
Water28816
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)123,49214
Polymers121,0974
Non-polymers2,39510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21210 Å2
ΔGint-174 kcal/mol
Surface area39990 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)125,88817
Polymers121,0974
Non-polymers4,79113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20160 Å2
ΔGint-163 kcal/mol
Surface area39640 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)96.505, 137.836, 273.451
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, EC: 1.3.99.1
#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, EC: 1.3.99.1
#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 , 11 types, 39 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#13: Chemical ChemComp-HQO / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / 2-HEPTYL-1-OXY-QUINOLIN-4-OL


Mass: 259.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21NO2
#14: Chemical
ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT


Mass: 538.755 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C28H58O9
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 5K MME, MgOAc, NaCitrate, EDTA, DTT, HQNO, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 5.8
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1999
RadiationMonochromator: 0.87 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 292370 / Num. obs: 292370 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.74 Å / % possible all: 74
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 93174 / Num. measured all: 292370 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 74 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: PDB entry 1FUM

1fum
PDB Unreleased entry


Resolution: 2.7→20 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.28 1953 random
Rwork0.231 --
all-292370 -
obs-292370 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16640 0 415 16 17071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.95
X-RAY DIFFRACTIONc_bond_d0.0193
Software
*PLUS
Name: 'CNS AND REFMAC' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.231 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0193

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