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- PDB-6awf: Escherichia coli quinol:fumarate reductase crystallized without d... -

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Basic information

Entry
Database: PDB / ID: 6awf
TitleEscherichia coli quinol:fumarate reductase crystallized without dicarboxylate
Components(Fumarate reductase ...) x 4
KeywordsELECTRON TRANSPORT / Complex II / quinol:fumarate reductase / fumarate reductase / succinate dehydrogenase / succinate oxidase / succinate:quinone oxidoreductase / FAD / flavoprotein / flavoenzyme
Function / homology
Function and homology information


: / : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding ...: / : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 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 / membrane => GO:0016020 / 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 / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin ...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 / 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 / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 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 / 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
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHATE ION / IRON/SULFUR CLUSTER / Fumarate reductase subunit D / Fumarate reductase subunit C / Fumarate reductase flavoprotein subunit / Fumarate reductase iron-sulfur subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsIverson, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061606 United States
Department of Veterans AffairsBX001077 United States
CitationJournal: J. Struct. Biol. / Year: 2018
Title: New crystal forms of the integral membrane Escherichia coli quinol:fumarate reductase suggest that ligands control domain movement.
Authors: Starbird, C.A. / Tomasiak, T.M. / Singh, P.K. / Yankovskaya, V. / Maklashina, E. / Eisenbach, M. / Cecchini, G. / Iverson, T.M.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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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 subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
E: Fumarate reductase flavoprotein subunit
F: Fumarate reductase iron-sulfur subunit
G: Fumarate reductase subunit C
H: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,60218
Polymers242,1948
Non-polymers3,40810
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)122,8019
Polymers121,0974
Non-polymers1,7045
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17200 Å2
ΔGint-169 kcal/mol
Surface area39010 Å2
MethodPISA
2
E: Fumarate reductase flavoprotein subunit
F: Fumarate reductase iron-sulfur subunit
G: Fumarate reductase subunit C
H: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8019
Polymers121,0974
Non-polymers1,7045
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16900 Å2
ΔGint-166 kcal/mol
Surface area36070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.318, 117.986, 125.291
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

#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, b4154, JW4115 / Production host: Escherichia coli (E. coli) / References: UniProt: P00363, fumarate reductase (quinol)
#2: Protein Fumarate reductase iron-sulfur subunit


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, Z5760, ECs5134 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC49, succinate dehydrogenase
#3: Protein Fumarate reductase subunit C / 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, ECS88_4740 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MKV9
#4: Protein Fumarate reductase subunit D / 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, ECS88_4739 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MKV8

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Non-polymers , 5 types, 10 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Fe2S2
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Fe3S4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 15% PEG 550 MME, 25 mM CaCl2, 50 mM Bis-tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.13 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 42318 / % possible obs: 89.8 % / Redundancy: 2.7 % / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF6

1kf6


Resolution: 3.35→46.912 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.55
RfactorNum. reflection% reflection
Rfree0.3181 3295 4.68 %
Rwork0.2847 --
obs0.2862 70448 76.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.35→46.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15715 0 116 0 15831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116222
X-RAY DIFFRACTIONf_angle_d1.5722071
X-RAY DIFFRACTIONf_dihedral_angle_d20.7655755
X-RAY DIFFRACTIONf_chiral_restr0.0672443
X-RAY DIFFRACTIONf_plane_restr0.0082814
Refinement TLS params.Method: refined / Origin x: 127.7366 Å / Origin y: 13.9419 Å / Origin z: 60.226 Å
111213212223313233
T0.6628 Å20.0085 Å2-0.0408 Å2-0.3768 Å2-0.0271 Å2--0.6908 Å2
L0.6726 °20.0408 °20.0339 °2-0.4206 °2-0.3761 °2--1.1246 °2
S0.0522 Å °-0.009 Å °0.0885 Å °-0.0118 Å °-0.046 Å °-0.0335 Å °-0.0218 Å °0.0767 Å °0.0014 Å °
Refinement TLS groupSelection details: all

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