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- PDB-2b76: E. coli Quinol fumarate reductase FrdA E49Q mutation -

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Basic information

Entry
Database: PDB / ID: 2b76
TitleE. coli Quinol fumarate reductase FrdA E49Q mutation
Components(Fumarate reductase ...) x 4
KeywordsOXIDOREDUCTASE / fumarate reductase / succinate dehydrogenase / electron transfer / respiration / krebs cycle / membrane protein
Function / homology
Function and homology information


fumarate reductase complex / fumarate reductase (quinol) / : / fermentation / succinate dehydrogenase activity / fumarate metabolic process / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic electron transport chain / anaerobic respiration ...fumarate reductase complex / fumarate reductase (quinol) / : / 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
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / CITRATE ANION / MENAQUINONE-7 / IRON/SULFUR CLUSTER / : / Fumarate reductase flavoprotein subunit / Fumarate reductase iron-sulfur subunit / Fumarate reductase subunit C ...FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / CITRATE ANION / MENAQUINONE-7 / IRON/SULFUR CLUSTER / : / Fumarate reductase flavoprotein subunit / Fumarate reductase iron-sulfur 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 / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMaklashina, E. / Iverson, T.M. / Sher, Y. / Kotlyar, V. / Mirza, O. / Andrell, J. / Hudson, J.M. / Armstrong, F.A. / Cecchini, G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Fumarate Reductase and Succinate Oxidase Activity of Escherichia coli Complex II Homologs Are Perturbed Differently by Mutation of the Flavin Binding Domain
Authors: Maklashina, E. / Iverson, T.M. / Sher, Y. / Kotlyar, V. / Andrell, J. / Mirza, O. / Hudson, J.M. / Armstrong, F.A. / Rothery, R.A. / Weiner, J.H. / Cecchini, G.
History
DepositionOct 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur protein
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur protein
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,08620
Polymers242,1928
Non-polymers4,89412
Water00
1
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur protein
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,54310
Polymers121,0964
Non-polymers2,4476
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18510 Å2
ΔGint-152 kcal/mol
Surface area40820 Å2
MethodPISA, PQS
2
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur protein
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,54310
Polymers121,0964
Non-polymers2,4476
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18420 Å2
ΔGint-155 kcal/mol
Surface area44080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.802, 139.527, 273.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a single heterotetramer. There are two heterotetramers 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: 66056.570 Da / Num. of mol.: 2 / Mutation: E49Q
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: GenBank: P00363, UniProt: P00363*PLUS
#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: P00364, UniProt: P0AC47*PLUS, EC: 1.3.99.1
#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 / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0A8Q0
#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 / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0A8Q3

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Non-polymers , 6 types, 12 molecules

#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#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.: 2 / Source method: obtained synthetically / Formula: C46H64O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Mg Acetate, PEG 5000 MME, Na Citrate, EDTA, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 47106 / % possible obs: 88.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.098
Reflection shellResolution: 3.3→3.35 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.1 / % possible all: 73.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1KF6

1kf6


Resolution: 3.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 921 1.6 %selected to be identical to 1KFY, 1KF6, 1L0V
Rwork0.248 ---
obs-47106 83.5 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 51.505 Å2
Baniso -1Baniso -2Baniso -3
1-4.427 Å20 Å20 Å2
2---0.241 Å20 Å2
3----4.186 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16606 0 234 0 16840
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2qfr.par
X-RAY DIFFRACTION3mq7.par

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