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- PDB-7bbt: Structure of cytochrome c in complex with a p-benzyl-sulfonato-ca... -

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Basic information

Entry
Database: PDB / ID: 7bbt
TitleStructure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / extended-arm / molecular recognition / biohybrid / alpha-helix
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Chem-T8W / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.023 Å
AuthorsMockler, N.M. / Ramberg, K. / Guagnini, F. / Raston, C.L. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2021
Title: Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with alpha-Helical Recognition Properties.
Authors: Mockler, N.M. / Ramberg, K.O. / Guagnini, F. / Raston, C.L. / Crowley, P.B.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c iso-1
B: Cytochrome c iso-1
C: Cytochrome c iso-1
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,77812
Polymers48,1674
Non-polymers10,6118
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-94 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.851, 70.215, 70.175
Angle α, β, γ (deg.)90.000, 102.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cytochrome c iso-1


Mass: 12041.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-T8W / 4-[[49,50,51,52,53,54,55,56-octahydroxy-11,17,23,29,35,41,47-heptakis[(4-sulfonatophenyl)methyl]-5-nonacyclo[43.3.1.13,7.19,13.115,19.121,25.127,31.133,37.139,43]hexapentaconta-1(49),3,5,7(56),9,11,13(55),15,17,19(54),21,23,25(53),27,29,31(52),33,35,37(51),39,41,43(50),45,47-tetracosaenyl]methyl]benzenesulfonate / p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane


Mass: 2202.398 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C112H88O32S8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350 200mM Ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 3.02→50.57 Å / Num. obs: 10928 / % possible obs: 96.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 90.54 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.093 / Rrim(I) all: 0.241 / Net I/σ(I): 8.9 / Num. measured all: 73389 / Scaling rejects: 2369
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.02-3.196.11.1531009316500.8550.5041.262399.8
9.56-50.575.20.0619893820.9950.0290.06714.698.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
BUSTER2.10.3 (18-SEP-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RSL

6rsl


Resolution: 3.023→50.57 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.479
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 502 4.63 %RANDOM
Rwork0.2334 ---
obs0.2346 10831 95.4 %-
Displacement parametersBiso max: 114.35 Å2 / Biso mean: 75.3 Å2 / Biso min: 26.66 Å2
Baniso -1Baniso -2Baniso -3
1--34.7443 Å20 Å2-9.2754 Å2
2--14.8287 Å20 Å2
3---19.9156 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 3.023→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 715 40 4119
Biso mean--76.48 54.66 -
Num. residues----428
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1551SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1166HARMONIC5
X-RAY DIFFRACTIONt_it4252HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion431SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2974SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4252HARMONIC20.005
X-RAY DIFFRACTIONt_angle_deg5824HARMONIC20.65
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion15.11
LS refinement shellResolution: 3.023→3.06 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3209 18 4.15 %
Rwork0.2646 416 -
obs--99.77 %

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