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- PDB-7tce: Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 wit... -

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Basic information

Entry
Database: PDB / ID: 7tce
TitleCrystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Respiratory Chain Complex III / Anti-malarial Atovaquone / Rhodobacter Spaheroides bc1 / Inhibition / MEMBRANE PROTEIN
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 / membrane / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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 / 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 / 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 / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-AOQ / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / STRONTIUM ION / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsEsser, L. / Xia, D. / Zhou, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.
Authors: Esser, L. / Xia, D. / Zhou, F.
History
DepositionDec 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
E: Cytochrome b
F: Cytochrome c1
G: Ubiquinol-cytochrome c reductase iron-sulfur subunit
K: Cytochrome b
L: Cytochrome c1
M: Ubiquinol-cytochrome c reductase iron-sulfur subunit
O: Cytochrome b
P: Cytochrome c1
Q: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,47246
Polymers397,55912
Non-polymers12,91334
Water00
1
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
E: Cytochrome b
F: Cytochrome c1
G: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,32424
Polymers198,7806
Non-polymers6,54418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31170 Å2
ΔGint-401 kcal/mol
Surface area71040 Å2
MethodPISA
2
K: Cytochrome b
L: Cytochrome c1
M: Ubiquinol-cytochrome c reductase iron-sulfur subunit
O: Cytochrome b
P: Cytochrome c1
Q: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,14922
Polymers198,7806
Non-polymers6,36916
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31220 Å2
ΔGint-401 kcal/mol
Surface area71130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.273, 156.388, 141.407
Angle α, β, γ (deg.)90.000, 96.670, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 3 through 2001)
21chain E
31(chain K and resid 3 through 2001)
41chain O
12chain B
22chain F
32chain L
42chain P
13chain C
23chain G
33chain M
43chain Q

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 3 through 2001)A3 - 2001
211chain EE3 - 2001
311(chain K and resid 3 through 2001)K3 - 2001
411chain OO3 - 2001
112chain BB1 - 2002
212chain FF1 - 2002
312chain LL1 - 2002
412chain PP1 - 2010
113chain CC9 - 1001
213chain GG9 - 1001
313chain MM9 - 1001
413chain QQ9 - 1001

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 12 molecules AEKOBFLPCGMQ

#1: Protein
Cytochrome b


Mass: 50087.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: petB, fbcB / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: Q02761
#2: Protein
Cytochrome c1


Mass: 29373.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: A3PFR5
#3: Protein
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 19928.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: petA, fbcF / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: Q02762, quinol-cytochrome-c reductase

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Sugars , 1 types, 4 molecules

#8: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 30 molecules

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


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-AOQ / 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione / Atovaquone


Mass: 366.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H19ClO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Chemical
ChemComp-6PE / 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 410.420 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H33NO8P
#7: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sr
#9: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#10: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Has ligand of interestY
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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7% PEG400, 200 MM HISTIDINE, 150 MM NACL, 10 MM SODIUM ASCORBATE, Atovaquone 5 fold molar excess, B-OG, SUCROSE MONO CAPARATE, TRIS PH 8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 50477 / % possible obs: 94.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 152.55 Å2 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.096 / Rrim(I) all: 0.223 / Χ2: 1.007 / Net I/σ(I): 3.9 / Num. measured all: 242827
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.85-3.942.90.8126810.340.4790.950.73676.3
3.94-4.043.30.75129870.3080.4220.8690.72684.4
4.04-4.153.60.66931370.5460.3630.7680.79487.9
4.15-4.273.70.61231500.730.330.70.82789
4.27-4.413.90.53932120.7650.2890.6160.9291.1
4.41-4.564.50.48833820.8430.2410.5481.06295.8
4.56-4.755.10.41934810.9140.1960.4651.06997.4
4.75-4.965.40.43235310.9180.1980.4771.01599.7
4.96-5.225.60.40435350.920.1830.4461.00899.9
5.22-5.555.50.37535410.9330.1720.4150.98799.8
5.55-5.985.30.31435510.9450.1470.3481.03299.6
5.98-6.584.80.25735470.9590.1260.2881.12299.4
6.58-7.5360.1835910.9860.0780.1971.14699.9
7.53-9.476.10.13335510.9870.0580.1461.06799.9
9.47-505.40.14836000.9860.0720.1661.03998.3

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Processing

Software
NameVersionClassification
SCALEPACK0.98.7214data scaling
PHENIX1.20_4444refinement
PDB_EXTRACT3.27data extraction
HKL-20000.98.7214data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kkz

5kkz


Resolution: 3.85→39.43 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0.37 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 1467 2.97 %
Rwork0.2407 47882 -
obs0.2417 49349 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 475.04 Å2 / Biso mean: 192.085 Å2 / Biso min: 108.4 Å2
Refinement stepCycle: final / Resolution: 3.85→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26956 0 1514 0 28470
Biso mean--192.18 --
Num. residues----3456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8271X-RAY DIFFRACTION5.579TORSIONAL
12E8271X-RAY DIFFRACTION5.579TORSIONAL
13K8271X-RAY DIFFRACTION5.579TORSIONAL
14O8271X-RAY DIFFRACTION5.579TORSIONAL
21B4950X-RAY DIFFRACTION5.579TORSIONAL
22F4950X-RAY DIFFRACTION5.579TORSIONAL
23L4950X-RAY DIFFRACTION5.579TORSIONAL
24P4950X-RAY DIFFRACTION5.579TORSIONAL
31C3368X-RAY DIFFRACTION5.579TORSIONAL
32G3368X-RAY DIFFRACTION5.579TORSIONAL
33M3368X-RAY DIFFRACTION5.579TORSIONAL
34Q3368X-RAY DIFFRACTION5.579TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.85-3.990.33311280.35094095422381
3.99-4.150.33161350.3374378451387
4.15-4.340.34721350.32474453458889
4.34-4.560.33841470.29634791493894
4.56-4.850.32531510.27234932508398
4.85-5.220.31321540.263650425196100
5.22-5.750.28241540.258950465200100
5.75-6.570.30721530.2525036518999
6.58-8.270.2441560.205350665222100
8.27-39.430.20731540.17965043519797

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