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- PDB-1l0v: Quinol-Fumarate Reductase with Menaquinol Molecules -

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Basic information

Entry
Database: PDB / ID: 1l0v
TitleQuinol-Fumarate Reductase with Menaquinol Molecules
Components(Fumarate reductase ...) x 4
KeywordsOXIDOREDUCTASE / fumarate reductase / succinate dehydrogenase / complex II / quinol / membrane protein
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
O-DODECANYL OCTAETHYLENE GLYCOL / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / MENAQUINONE-7 / 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 / MAD / Resolution: 3.3 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 E. coli Fumarate Reductase Respiratory Complex
Authors: Iverson, T.M. / Luna-Chavez, C. / Cecchini, G. / Rees, D.C.
#2: Journal: Protein Expr.Purif. / Year: 2000
Title: Overexpression, Purification, and Crystallization of the Membrane-Bound Fumarate Reductase from Eschericia coli
Authors: Luna-Chavez, C. / Iverson, T.M. / Rees, D.C. / Cecchini, G.
History
DepositionFeb 13, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionMar 13, 2002ID: 1fum
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 / 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 / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Fumarate reductase iron-sulfur protein
C: Fumarate reductase 15 kDa hydrophobic protein
D: Fumarate reductase 13 kDa hydrophobic protein
M: Fumarate reductase flavoprotein subunit
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)250,42526
Polymers242,1948
Non-polymers8,23118
Water00
1
A: Fumarate reductase flavoprotein subunit
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)125,21213
Polymers121,0974
Non-polymers4,1159
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19870 Å2
ΔGint-161 kcal/mol
Surface area39590 Å2
MethodPISA
2
M: Fumarate reductase flavoprotein subunit
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)125,21213
Polymers121,0974
Non-polymers4,1159
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20850 Å2
ΔGint-158 kcal/mol
Surface area41380 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)96.590, 138.090, 275.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsheterotetramer: two complete heterotetramers are observed in each asymmetric unit

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Components

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

#1: Protein Fumarate reductase flavoprotein subunit


Mass: 66057.555 Da / Num. of mol.: 2
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 protein


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 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) / Gene: FrdC / Plasmid: pH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / 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) / Gene: FrdD / Plasmid: pH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0A8Q3

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Non-polymers , 7 types, 18 molecules

#5: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#6: Chemical ChemComp-FAD / 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


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


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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C46H64O2
#11: Chemical
ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT


Mass: 538.755 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H58O9

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Details

Has protein modificationY

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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: 3.79 Å3/Da / Density % sol: 67.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 10000, MgAcetate, NaCitrate, DTT, EDTA, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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: ALS / Beamline: 5.0.2 / Wavelength: 1.65 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 49332 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 75 Å2 / Rsym value: 0.093 / Net I/σ(I): 15.5
Reflection shellResolution: 3.3→3.42 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.277 / % possible all: 90
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 219456 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 6.3

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1FUM

1fum
PDB Unreleased entry


Resolution: 3.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.29 1005 random
Rwork0.245 --
obs-49332 -
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16640 0 406 0 17046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.015
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.245 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.014

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