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

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Basic information

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 / homology
Function and homology information


succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding ...succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #820 / Fumarate reductase type B, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit ...Ubiquitin-like (UB roll) - #820 / Fumarate reductase type B, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / 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 / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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 / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / 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 / 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 / PROTOPORPHYRIN IX CONTAINING FE / MALONIC ACID / IRON/SULFUR CLUSTER / Fumarate reductase flavoprotein subunit / Fumarate reductase cytochrome b subunit / Fumarate reductase iron-sulfur subunit
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
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.
History
DepositionSep 1, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Apr 22, 2015Group: Non-polymer description
Revision 2.0Nov 21, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / entity_src_nat / pdbx_unobs_or_zero_occ_atoms / struct_ref
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
Polymers519,12212
Non-polymers13,91836
Water00
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
Polymers259,5616
Non-polymers6,95918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38830 Å2
ΔGint-362.5 kcal/mol
Surface area76100 Å2
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
Polymers259,5616
Non-polymers6,95918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38830 Å2
ΔGint-359.8 kcal/mol
Surface area76090 Å2
MethodPISA
Unit cell
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-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.57768, -0.54733, -0.60557), (-0.5435, -0.2956, 0.78564), (-0.60901, 0.78297, -0.12672)-0.16689, -6.8204, 6.04004
2given(-0.42759, 0.00845, -0.90393), (-0.00563, -0.99996, -0.00669), (-0.90396, 0.00223, 0.42762)44.39704, 58.59339, 83.8085
3given(0.79356, -0.47221, 0.38377), (0.55227, 0.29417, -0.78004), (0.25545, 0.83095, 0.49423)39.00774, 65.35092, 86.57045

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Components

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

#1: Protein
Fumarate reductase flavoprotein subunit


Mass: 72825.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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
Fumarate reductase iron-sulfur subunit


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


Mass: 29758.070 Da / Num. of mol.: 4 / Mutation: E66Q
Source method: isolated from a genetically manipulated source
Details: HAEM AXIAL LIGANDS - HIS 44, HIS 93, HIS 143 HIS 182
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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Sugars , 1 types, 4 molecules

#11: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 7 types, 32 molecules

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


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


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical
ChemComp-NA / SODIUM ION


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


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


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


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Details

Compound detailsCHAINS: C, F, I, L CONTAIN ENGINEERED MUTATION E66Q
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: 3.46 Å3/Da / Density % 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
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mM1dropK3Fe(CN)6
20.05 %dodecyl-beta-D-maltoside1drop
30.20 %decylmaltoside1drop
42.4 %benzamidine1drop
55 %PEG33501drop
675 mM1dropNaCl
75 %DME1drop
81 mMDMN1drop
91 mMmalonate1drop
1010 mMHEPES1drop
1110 mMcitrate1droppH6.4
129.5 mg/mlprotein1drop
13150 mM1reservoirNaCl
1410 %PEG33501reservoir
1520 mMcitrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.958
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 9, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 102882 / % possible obs: 80.8 % / Observed criterion σ(I): -1 / Redundancy: 2.7 % / Biso Wilson estimate: 65.4 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.9
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 1.97 % / Mean I/σ(I) obs: 2 / Rsym value: 0.26 / % possible all: 61.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLA

1qla
PDB Unreleased entry


Resolution: 3.1→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: N(OBS)/N(PAR) = 1.57
RfactorNum. reflection% reflectionSelection details
Rfree0.291 750 0.7 %750 THIN SHELLS
Rwork0.283 ---
obs0.283 102882 80.8 %-
Solvent computationBsol: 48.4 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 84.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.66 Å
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36276 0 804 0 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_it0.9981.5
X-RAY DIFFRACTIONc_mcangle_it1.1162
X-RAY DIFFRACTIONc_scbond_it1.7952
X-RAY DIFFRACTIONc_scangle_it1.8762.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.454 95 0.7 %
Rwork0.477 12962 -
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
LS refinement shell
*PLUS
Rfactor obs: 0.477

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