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- PDB-4kx6: Plasticity of the quinone-binding site of the complex II homolog ... -

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Basic information

Entry
Database: PDB / ID: 4kx6
TitlePlasticity of the quinone-binding site of the complex II homolog quinol:fumarate reductase
Components(Fumarate reductase ...) x 4
KeywordsOXIDOREDUCTASE / Membrane Protein / Complex II homolog / FrdC-E29L
Function / homology
Function and homology information


plasma membrane fumarate reductase complex / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / bacterial-type flagellum assembly / FAD binding ...plasma membrane fumarate reductase complex / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / bacterial-type flagellum assembly / FAD binding / flavin adenine dinucleotide binding / electron transfer activity / DNA damage response / membrane / plasma membrane / cytosol
Similarity search - Function
Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 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, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 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 / 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 / FAD binding domain / Rhinovirus 14, subunit 4 / Beta-grasp domain / FAD/NAD(P)-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) / 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 / MENAQUINONE-7 / IRON/SULFUR CLUSTER / : / : / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSingh, P.K. / Sarwar, M. / Maklashina, E. / Kotlyar, V. / Rajagukguk, S. / Tomasiak, T.M. / Cecchini, G. / Iverson, T.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Plasticity of the Quinone-binding Site of the Complex II Homolog Quinol:Fumarate Reductase.
Authors: Singh, P.K. / Sarwar, M. / Maklashina, E. / Kotlyar, V. / Rajagukguk, S. / Tomasiak, T.M. / Cecchini, G. / Iverson, T.M.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 (Anaerobic), Fe-S subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase (Anaerobic), Fe-S subunit
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,51818
Polymers237,0038
Non-polymers4,51610
Water0
1
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase (Anaerobic), Fe-S subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7599
Polymers118,5014
Non-polymers2,2585
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18090 Å2
ΔGint-159 kcal/mol
Surface area39880 Å2
MethodPISA
2
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase (Anaerobic), Fe-S subunit
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7599
Polymers118,5014
Non-polymers2,2585
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18130 Å2
ΔGint-163 kcal/mol
Surface area40130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.093, 138.620, 273.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Fumarate reductase flavoprotein subunit


Mass: 63477.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: frdA, b4154, JW4115 / Production host: Escherichia coli (E. coli) / References: UniProt: P00363, succinate dehydrogenase
#2: Protein Fumarate reductase (Anaerobic), Fe-S subunit


Mass: 27021.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / MC4100 / BW2952 / Gene: frdB, BWG_3868 / Production host: Escherichia coli (E. coli) / References: UniProt: C5A1E7
#3: Protein Fumarate reductase subunit C / / Fumarate reductase 15 kDa hydrophobic protein


Mass: 14882.818 Da / Num. of mol.: 2 / Mutation: E29L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: frdC, EcDH1_3838, ECDH1ME8569_4012 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QU46
#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) / Strain: K12 / Gene: frdD, b4151, JW4112 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q3

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Non-polymers , 5 types, 10 molecules

#5: 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
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#9: Chemical ChemComp-MQ7 / MENAQUINONE-7 / Vitamin K2


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: 1

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 13%-15% PEG 5000 MME, 85mM-115mM Magnesium Acetate, 100mM Sodium Citrate, 0.01mM DTT, 0.1mM EDTA, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 295.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2012
RadiationMonochromator: 3.0 cm undulator using two Laue diamond monochromators and one 2.5 m large offset monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.95→47.8 Å / Num. obs: 75158 / % possible obs: 95.7 % / Observed criterion σ(F): 33.2 / Observed criterion σ(I): 116.3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.95-3.06194.5
3.06-3.18194.8
3.18-3.32194.9
3.32-3.5195.1
3.5-3.72195.4
3.72-4196.9
4-4.41197.9
4.41-5.04197.4
5.04-6.35196.8
6.35-50193.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→47.8 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.88 / SU B: 37.421 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 1.164 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27976 1322 1.8 %RANDOM
Rwork0.24016 ---
obs0.24087 73803 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 75.533 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å2-0 Å2
2---2.57 Å2-0 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16636 0 192 0 16828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01917254
X-RAY DIFFRACTIONr_bond_other_d0.0050.0216394
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.96623448
X-RAY DIFFRACTIONr_angle_other_deg0.791337644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.99752130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24523.512746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.821152810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.91115110
X-RAY DIFFRACTIONr_chiral_restr0.0530.22566
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02119442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024014
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1975.1948544
X-RAY DIFFRACTIONr_mcbond_other1.1975.1948543
X-RAY DIFFRACTIONr_mcangle_it2.1197.78510666
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8615.2518710
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.109 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.365 116 -
Rwork0.31 10499 -
obs--94.63 %
Refinement TLS params.Method: refined / Origin x: 20.8173 Å / Origin y: -6.7638 Å / Origin z: -31.1316 Å
111213212223313233
T0.1933 Å2-0.0686 Å20.1271 Å2-0.1532 Å20.0077 Å2--0.1455 Å2
L0.1806 °2-0.2233 °2-0.1954 °2-0.6676 °20.3474 °2--0.354 °2
S-0.1167 Å °-0.0246 Å °-0.0589 Å °0.0099 Å °0.0243 Å °0.0172 Å °0.1801 Å °-0.0851 Å °0.0924 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 576
2X-RAY DIFFRACTION1B1 - 243
3X-RAY DIFFRACTION1C1 - 130
4X-RAY DIFFRACTION1D0 - 118
5X-RAY DIFFRACTION1M0 - 576
6X-RAY DIFFRACTION1N1 - 243
7X-RAY DIFFRACTION1O1 - 130
8X-RAY DIFFRACTION1P0 - 118

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