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- PDB-1e7p: QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES -

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Entry
Database: PDB / ID: 1e7p
TitleQUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES
Components(Fumarate reductase ...) x 3
KeywordsOXIDOREDUCTASE / SUCCINATE DEHYDROGENASE / RESPIRATORY CHAIN / CITRIC ACID CYCLE / FLAVOPROTEIN / IRON- SULPHUR PROTEIN IRON- SULPHUR PROTEIN / DIHAEM CYTOCHROME B
Function / homologyBeta-grasp domain superfamily / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydogenase/fumarate reductase N-terminal / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / Succinate dehydrogenase/fumarate reductase iron-sulphur protein ...Beta-grasp domain superfamily / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydogenase/fumarate reductase N-terminal / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Fumarate reductase type B, transmembrane subunit / FAD-dependent oxidoreductase 2, FAD binding domain / Fumarate reductase/succinate dehydrogenase, FAD-binding site / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain superfamily / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / FAD binding domain / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase flavoprotein C-term / 2Fe-2S iron-sulfur cluster binding domain / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / fumarate reductase (quinol) / fumarate reductase (menaquinone) / succinate dehydrogenase / succinate dehydrogenase (ubiquinone) activity / oxidoreductase activity, acting on the CH-CH group of donors / electron transport chain / 3 iron, 4 sulfur cluster binding / respirasome / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity / integral component of membrane / plasma membrane / metal ion binding / Fumarate reductase flavoprotein subunit / Fumarate reductase cytochrome b subunit / Fumarate reductase iron-sulfur subunit
Function and homology information
Specimen sourceWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.1 Å resolution
AuthorsLancaster, C.R.D. / Kroeger, A.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: A Third Crystal Form of Wolinella Succinogenes Quinol:Fumarate Reductase Reveals Domain Closure at the Site of Fumarate Reduction
Authors: Lancaster, C.R.D. / Gross, R. / Simon, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Essential Role of Glu-C66 for Menaquinol Oxidation Indicates Transmembrane Electrochemical Potential Generation by Wolinella Succinogenes Fumarate Reductase
Authors: Lancaster, C.R.D. / Gross, R. / Haas, A. / Ritter, M. / Maentele, W. / Simon, J. / Kroeger, A.
#2: Journal: Nature / Year: 1999
Title: Structure of Fumarate Reductase from Wolinella Succinogenes at 2.2 Angstroms Resolution
Authors: Lancaster, C.R.D. / Kroeger, A. / Auer, M. / Michel, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 2000 / Release: Apr 9, 2001
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 9, 2001Structure modelrepositoryInitial release
1.1Apr 17, 2013Structure modelAtomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
1.2Apr 22, 2015Structure modelNon-polymer description
2.0Nov 21, 2018Structure modelAdvisory / Atomic model / Data collection / Database references / Source and taxonomy / Structure summaryatom_site / entity / entity_src_gen / entity_src_nat / pdbx_unobs_or_zero_occ_atoms / struct_ref_entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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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 cytochrome b subunit
D: Fumarate reductase flavoprotein subunit
E: Fumarate reductase iron-sulfur subunit
F: Fumarate reductase cytochrome b subunit
G: Fumarate reductase flavoprotein subunit
H: Fumarate reductase iron-sulfur subunit
I: Fumarate reductase cytochrome b subunit
J: Fumarate reductase flavoprotein subunit
K: Fumarate reductase iron-sulfur subunit
L: Fumarate reductase cytochrome b subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,04048
Polyers519,12212
Non-polymers13,91836
Water0
1
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur subunit
C: Fumarate reductase cytochrome b subunit
D: Fumarate reductase flavoprotein subunit
E: Fumarate reductase iron-sulfur subunit
F: Fumarate reductase cytochrome b subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,52024
Polyers259,5616
Non-polymers6,95918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)38830
ΔGint (kcal/M)-362.5
Surface area (Å2)76100
MethodPISA
2
G: Fumarate reductase flavoprotein subunit
H: Fumarate reductase iron-sulfur subunit
I: Fumarate reductase cytochrome b subunit
J: Fumarate reductase flavoprotein subunit
K: Fumarate reductase iron-sulfur subunit
L: Fumarate reductase cytochrome b subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,52024
Polyers259,5616
Non-polymers6,95918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)38830
ΔGint (kcal/M)-359.8
Surface area (Å2)76090
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)81.074, 290.240, 153.614
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Fumarate reductase ... , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein/peptide
Fumarate reductase flavoprotein subunit


Mass: 72825.055 Da / Num. of mol.: 4
Details: 8-ALPHA-[-N-EPSILON-HISTIDYL] COVALENT BOND BETWEEN FLAVIN ADENINE DINUCLEOTIDE (FAD) AND HIS 43
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: frdA, WS0831 / Production host: Wolinella succinogenes (bacteria) / References: UniProt: P17412, fumarate reductase (quinol)
#2: Protein/peptide
Fumarate reductase iron-sulfur subunit


Mass: 27197.453 Da / Num. of mol.: 4 / Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: frdB, WS0830 / Production host: Wolinella succinogenes (bacteria) / References: UniProt: P17596, succinate dehydrogenase
#3: Protein/peptide
Fumarate reductase cytochrome b subunit


Mass: 29758.070 Da / Num. of mol.: 4
Details: HAEM AXIAL LIGANDS - HIS 44, HIS 93, HIS 143 HIS 182
Mutation: E66Q / Source: (gene. exp.) Wolinella succinogenes (bacteria)
Strain: ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W
Gene: frdC, WS0832 / Variant: FRDC-E66Q / Production host: Wolinella succinogenes (bacteria) / References: UniProt: P17413

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Non-polymers , 8 types, 36 molecules

#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#5: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Formula: C3H4O4 / Malonic acid
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Formula: Na / Sodium
#7: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Formula: Fe2S2
#8: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Formula: Fe3S4
#9: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Formula: Fe4S4 / Iron–sulfur cluster
#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Formula: C34H32FeN4O4 / Heme
#11: Chemical
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Mass: 510.615 Da / Num. of mol.: 4 / Formula: C24H46O11 / Comment: detergent *YM

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Details

Compound detailsCHAINS: C, F, I, L CONTAIN ENGINEERED MUTATION E66Q

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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: 3.46 / Density percent sol: 64 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 6.4 / Method: vapor diffusion
Details: used microseeding, Lancaster, C.R.D., (1999) Nature, 402, 377.
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
11 mMdropK3Fe(CN)6
20.05 %dodecyl-beta-D-maltosidedrop
30.20 %decylmaltosidedrop
42.4 %benzamidinedrop
55 %PEG3350drop
675 mMdropNaCl
75 %DMEdrop
81 mMDMNdrop
91 mMmalonatedrop
1010 mMHEPESdrop
1110 mMcitratedroppH6.4
129.5 mg/mlproteindrop
13150 mMreservoirNaCl
1410 %PEG3350reservoir
1520 mMcitratereservoirpH5.6

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Data collection

DiffractionMean temperature: 275 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.958
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: CCD / Collection date: Jul 9, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 65.4 Å2 / D resolution high: 3.1 Å / D resolution low: 3 Å / Number obs: 102882 / Observed criterion sigma I: -1 / Rsym value: 0.06 / NetI over sigmaI: 11.9 / Redundancy: 2.7 % / Percent possible obs: 80.8
Reflection shellHighest resolution: 3.1 Å / Lowest resolution: 3.29 Å / MeanI over sigI obs: 2 / Rsym value: 0.26 / Redundancy: 1.97 % / Percent possible all: 61.7

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Processing

Software
NameVersionClassification
CNS1.0refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLA
Details: N(OBS)/N(PAR) = 1.57 / R Free selection details: 750 THIN SHELLS / Data cutoff high absF: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model param bsol: 48.4 / Solvent model param ksol: 0.31
Displacement parametersB iso mean: 84.8 Å2
Least-squares processR factor R free: 0.291 / R factor R free error: 0.011 / R factor R work: 0.283 / R factor obs: 0.283 / Highest resolution: 3.1 Å / Lowest resolution: 3 Å / Number reflection R free: 750 / Number reflection obs: 102882 / Percent reflection R free: 0.7 / Percent reflection obs: 80.8
Refine analyzeLuzzati coordinate error obs: 0.66 Å
Refine hist #LASTHighest resolution: 3.1 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 36276 / Nucleic acid: 0 / Ligand: 804 / Solvent: 0 / Total: 37080
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9981.50
X-RAY DIFFRACTIONc_mcangle_it1.1162.00
X-RAY DIFFRACTIONc_scbond_it1.7952.00
X-RAY DIFFRACTIONc_scangle_it1.8762.50
Refine LS shellHighest resolution: 3.1 Å / R factor R free: 0.454 / R factor R free error: 0.049 / R factor R work: 0.477 / Lowest resolution: 3.29 Å / Number reflection R free: 95 / Number reflection R work: 12962 / Total number of bins used: 10 / Percent reflection R free: 0.7 / Percent reflection obs: 61.7
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARHEM.ROYTOPHEM.ROY
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.73
Refine LS shell
*PLUS
R factor obs: 0.477

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