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- PDB-2yiu: X-ray structure of the dimeric cytochrome BC1 complex from the so... -

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Basic information

Entry
Database: PDB / ID: 2yiu
TitleX-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution
Components
  • CYTOCHROME B
  • CYTOCHROME C1, HEME PROTEIN
  • UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / STIGMATELLIN A / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1
Similarity search - Component
Biological speciesPARACOCCUS DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKleinschroth, T. / Castellani, M. / Trinh, C.H. / Morgner, N. / Brutschy, B. / Ludwig, B. / Hunte, C.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: X-Ray Structure of the Dimeric Cytochrome Bc(1) Complex from the Soil Bacterium Paracoccus Denitrificans at 2.7-A Resolution.
Authors: Kleinschroth, T. / Castellani, M. / Trinh, C.H. / Morgner, N. / Brutschy, B. / Ludwig, B. / Hunte, C.
History
DepositionMay 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Dec 20, 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 / struct_conn / struct_conn_type / 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 / _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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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: CYTOCHROME B
B: CYTOCHROME C1, HEME PROTEIN
C: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
D: CYTOCHROME B
E: CYTOCHROME C1, HEME PROTEIN
F: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,78316
Polymers200,6996
Non-polymers5,08410
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28390 Å2
ΔGint-336.7 kcal/mol
Surface area66310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.300, 164.910, 100.610
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein CYTOCHROME B


Mass: 51536.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: C-TERMINAL DECA-HIS TAG / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Variant: MK6 PMC1 (FBC-OPERON) / Strain: PD1222 / References: UniProt: P05418, quinol-cytochrome-c reductase
#2: Protein CYTOCHROME C1, HEME PROTEIN


Mass: 28491.744 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-450 / Source method: isolated from a natural source
Details: DELETION OF AMINO ACIDS 39 TO 201 COMPARED TO WILD-TYPE
Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Variant: MK6 PMC1 (FBC-OPERON) / Strain: PD1222 / References: UniProt: P13627, quinol-cytochrome-c reductase
#3: Protein UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE / RIESKE IRON-SULFUR PROTEIN / RISP


Mass: 20321.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Variant: MK6 PMC1 (FBC-OPERON) / Strain: PD1222 / References: UniProt: P05417, quinol-cytochrome-c reductase

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Non-polymers , 5 types, 16 molecules

#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42O7
#6: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEC): HEME C PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME B
Sequence detailsNO C-TERMINAL DECA-HIS TAG IN THE DATABANK SEQUENCE. AMINO ACIDS 39-201(CHAINS B AND E) WERE ...NO C-TERMINAL DECA-HIS TAG IN THE DATABANK SEQUENCE. AMINO ACIDS 39-201(CHAINS B AND E) WERE DELETED IN THE MUTANT COMPARED TO THE WILD-TYPE SEQUENCE IN THE DATABASE. THE SEQUENCE BELOW IS THE ONE OF THE DELETION VARIANT. CHAIN, B, E. NUMBERING OF SUBUNIT CYT C1DELTAAC INCLUDES THE PREDICTED SIGNAL SEQUENCE (RESIDUES 1-24), BUT LACKS THE SEQUENCE FOR THE ACIDIC DOMAIN OF WILD-TYPE CYT C1 (RESIDUES 39-201 OF WILD-TYPE CYT C1).

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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: 3.59 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE, PH 4.6, 50 MM NACL, 30% 2-METHYL 2,4-PENTANDIOL (MPD)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 8, 2009 / Details: KIRKPATRICK-BAEZ MIRROR PAIR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR TWO SI III CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→54.97 Å / Num. obs: 70055 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 3.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QJY

2qjy


Resolution: 2.7→97.96 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.886 / SU B: 11.368 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.629 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29049 3535 5 %RANDOM
Rwork0.23766 ---
obs0.24033 66493 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.805 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0.22 Å2
2--0.47 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.7→97.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12644 0 340 6 12990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213438
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7612.00618454
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76451606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03223.2550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.929151898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6681558
X-RAY DIFFRACTIONr_chiral_restr0.1030.21970
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110368
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6731.58034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.267212936
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94235404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0214.55514
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 258 -
Rwork0.279 4683 -
obs--89.71 %

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