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- PDB-2qjp: Crystal structure of wild type rhodobacter sphaeroides with stigm... -

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Basic information

Entry
Database: PDB / ID: 2qjp
TitleCrystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsELECTRON TRANSPORT / Cytochrome b with 8 TM helices / one c-term TM in cytochrome c1 and an N-term TM in the iron-sulfur-protein (Rieske) / Heme / Membrane / Metal-binding / Respiratory chain / Transmembrane / Transport / 2Fe-2S / Inner membrane / Oxidoreductase
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / intracellular membrane-bounded organelle / heme binding / membrane ...respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding / plasma membrane / cytoplasm
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 Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / 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 Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b / : / : / 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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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] iron-sulphur domain / Rieske [2Fe-2S] 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
Chem-ANJ / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-LOP / STIGMATELLIN A / STRONTIUM ION / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome c1
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEsser, L. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Inhibitor-complexed structures of the cytochrome bc1 from the photosynthetic bacterium Rhodobacter sphaeroides.
Authors: Esser, L. / Elberry, M. / Zhou, F. / Yu, C.A. / Yu, L. / Xia, D.
History
DepositionJul 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,59850
Polymers380,90112
Non-polymers16,69738
Water3,765209
1
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,71124
Polymers190,4506
Non-polymers8,26118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31440 Å2
MethodPISA
2
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,88626
Polymers190,4506
Non-polymers8,43620
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.061, 146.520, 141.003
Angle α, β, γ (deg.)90.00, 110.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Cytochrome b /


Mass: 48367.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petB, fbcB / Plasmid: pRKDfbcFBCQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q02761
#2: Protein
Cytochrome c1 /


Mass: 27786.162 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: fbcC / Plasmid: pRKDfbcFBCQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IY11, UniProt: Q02760*PLUS
#3: Protein
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 19071.494 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Plasmid: pRKDfbcFBCQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q02762, quinol-cytochrome-c reductase

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 243 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H42O7
#7: Chemical
ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


Mass: 661.890 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H68NO8P / Comment: phospholipid*YM
#8: Chemical
ChemComp-ANJ / (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE


Mass: 548.625 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H40N2O9
#9: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sr
#10: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM Tris, 0.5% b-OG, 0.12% Sucrosemonocaprate, 6.39% PEG400, 1.50% PEG3350, 10 mM Strontium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.75 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2006 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 157560 / Num. obs: 156392 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1.5 / Redundancy: 4.5 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 10.51
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.42 / Num. unique all: 14848 / Rsym value: 0.67 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FYN

2fyn


Resolution: 2.6→17.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3101164.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: NCS restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3027 2 %SHELLS
Rwork0.244 ---
obs0.244 154627 98 %-
all-154627 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4758 Å2 / ksol: 0.335398 e/Å3
Displacement parametersBiso mean: 78.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.06 Å20 Å223.46 Å2
2---13.43 Å20 Å2
3---7.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.6→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26916 0 1102 209 28227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.71
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it0.82
X-RAY DIFFRACTIONc_scangle_it1.312.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 478 1.9 %
Rwork0.405 24481 -
obs-26454 95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_MET.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3Ligand.parLigand.top
X-RAY DIFFRACTION4cis_peptide.paramwater.top
X-RAY DIFFRACTION5water_rep.param

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