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- PDB-2bs3: GLU C180 -> GLN VARIANT QUINOL:FUMARATE REDUCTASE FROM WOLINELLA ... -

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Basic information

Entry
Database: PDB / ID: 2bs3
TitleGLU C180 -> GLN VARIANT QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES
Components(QUINOL-FUMARATE REDUCTASE ...) x 3
KeywordsOXIDOREDUCTASE / 2FE-2S / 3FE-4S / 4FE-4S / CITRIC ACID CYCLE / DIHAEM CYTOCHROME B / ELECTRON TRANSPORT / FAD / FLAVOPROTEIN / FUMARATE REDUCTASE / HEME / ION-SULPHUR PROTEIN / IRON / IRON- SULFUR / METAL-BINDING / RESPIRATORY CHAIN / SUCCINATE DEHYDROGENASE / TRANSMEMBRANE / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


: / succinate dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / respirasome / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding ...: / succinate dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / respirasome / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer 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 / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase 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 ...Ubiquitin-like (UB roll) - #820 / Fumarate reductase type B, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase 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 / 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 / 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. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-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
CITRIC ACID / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / 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: 2.19 Å
AuthorsLancaster, C.R.D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Experimental Support for the E-Pathway Hypothesis of Coupled Transmembrane Electron and Proton Transfer in Dihemic Quinol:Fumarate Reductase
Authors: Lancaster, C.R.D. / Sauer, U.S. / Gross, R. / Haas, A.H. / Graf, J. / Schwalbe, H. / Maentele, W. / Simon, J. / Madej, G.
#1: Journal: FEBS Lett. / Year: 2003
Title: Wolinella Succinogenes Quinol:Fumarate Reductase and its Comparison to E. Coli Succinate:Quinone Reductase
Authors: Lancaster, C.R.D.
#2: Journal: Biochim.Biophys.Acta / Year: 2002
Title: Wolinella Succinogenes Quinol:Fumarate Reductase -2.2 Angstrom Resolution Crystal Structure and the E-Pathway Hypothesis of Coupled Transmembrane Proton and Electron Transfer
Authors: Lancaster, C.R.D.
#3: 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.
#4: 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.
#5: 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
DepositionMay 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...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 / struct_conn
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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QUINOL-FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT A
B: QUINOL-FUMARATE REDUCTASE IRON-SULFUR SUBUNIT B
C: QUINOL-FUMARATE REDUCTASE DIHEME CYTOCHROME B SUBUNIT C
D: QUINOL-FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT A
E: QUINOL-FUMARATE REDUCTASE IRON-SULFUR SUBUNIT B
F: QUINOL-FUMARATE REDUCTASE DIHEME CYTOCHROME B SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,69624
Polymers259,5616
Non-polymers7,13518
Water17,853991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.104, 188.766, 117.817
Angle α, β, γ (deg.)90.00, 104.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.011239, 0.003138), (0.010826, -0.793178, 0.608894), (-0.004354, 0.608886, 0.793246)
Vector: 174.4428, -1.514, 0.7045)

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Components

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QUINOL-FUMARATE REDUCTASE ... , 3 types, 6 molecules ADBECF

#1: Protein QUINOL-FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT A


Mass: 72825.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: FAD COVALENTLY BOUND TO HIS A43 BY AN 8-ALPHA-(N-EPSILON-HISTIDYL) BOND
Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17412, succinate dehydrogenase
#2: Protein QUINOL-FUMARATE REDUCTASE IRON-SULFUR SUBUNIT B


Mass: 27197.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17596, succinate dehydrogenase
#3: Protein QUINOL-FUMARATE REDUCTASE DIHEME CYTOCHROME B SUBUNIT C


Mass: 29758.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17413, succinate dehydrogenase

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Sugars , 1 types, 2 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 1007 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 991 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: ESSENTIAL FOR FUMARATE RESPIRATION
Sequence detailsAUTHORS SAY CONFLICT GLN 180 GLU FOR CHAINS C, F IS A VARIANT

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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: 62.4 %
Crystal growpH: 6 / Details: pH 6.00

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.19→38.6 Å / Num. obs: 182229 / % possible obs: 99.8 % / Observed criterion σ(I): -1 / Redundancy: 5.3 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 7.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BS2

2bs2


Resolution: 2.19→38.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2855917.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1000 0.5 %SHELLS
Rwork0.183 ---
obs0.183 182197 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4032 Å2 / ksol: 0.309923 e/Å3
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å22.8 Å2
2---2.93 Å20 Å2
3---2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.19→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18138 0 414 991 19543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.19→2.24 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.257 58 0.6 %
Rwork0.22 10372 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3PARHEM.ROYTOPHEM.ROY
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5CIT.PARCIT.TOP

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