[English] 日本語
Yorodumi
- PDB-1kfy: QUINOL-FUMARATE REDUCTASE WITH QUINOL INHIBITOR 2-[1-(4-CHLORO-PH... -

+
Open data


ID or keywords:

Loading...

-
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


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
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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

-
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

-
Non-polymers , 7 types, 15 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-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


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more