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- PDB-6rgi: Partially unfolded cytochrome c in complex with sulfonatocalix[6]arene -

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Basic information

Entry
Database: PDB / ID: 6rgi
TitlePartially unfolded cytochrome c in complex with sulfonatocalix[6]arene
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / molecular glues / calixarene / protein assembly / supramolecular chemistry
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / 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
p-sulfonatocalix[6]arene / HEME C / IMIDAZOLE / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsEngilberge, S. / Rennie, M.L. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: Febs Lett. / Year: 2019
Title: Calixarene capture of partially unfolded cytochrome c.
Authors: Engilberge, S. / Rennie, M.L. / Crowley, P.B.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8404
Polymers12,0421
Non-polymers1,7993
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-15 kcal/mol
Surface area5970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.762, 74.762, 60.033
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome c iso-1


Mass: 12041.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-FWQ / p-sulfonatocalix[6]arene


Mass: 1111.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H30O24S6
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 4.7 Å3/Da / Density % sol: 65 % / Description: long rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 11 % PEG 8000, 0.1 M imidazole, 2 mM sulfonato-calix[6]arene

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.981 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.64→44.02 Å / Num. obs: 3582 / % possible obs: 91 % / Redundancy: 17.9 % / Biso Wilson estimate: 107.85 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.022 / Rrim(I) all: 0.094 / Net I/σ(I): 1.3
Reflection shellResolution: 2.64→2.94 Å / Rmerge(I) obs: 1.46 / Num. unique obs: 200 / Rpim(I) all: 0.482 / Rrim(I) all: 1.55

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LYC

5lyc


Resolution: 2.64→44.02 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.385
RfactorNum. reflection% reflectionSelection details
Rfree0.25 191 5.34 %RANDOM
Rwork0.2 ---
obs0.202 3580 60.3 %-
Displacement parametersBiso max: 218.42 Å2 / Biso mean: 93.18 Å2 / Biso min: 32.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.9896 Å20 Å20 Å2
2--1.9896 Å20 Å2
3----3.9791 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.64→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 120 21 867
Biso mean--73.19 64.84 -
Num. residues----92
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d341SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes256HARMONIC5
X-RAY DIFFRACTIONt_it1603HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion92SEMIHARMONIC5
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_contact1596SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1603HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2875HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion17.53
LS refinement shellResolution: 2.64→2.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3851 4 1.91 %
Rwork0.253 205 -
all0.2544 209 -
obs--12.6 %
Refinement TLS params.Method: refined / Origin x: -31.9339 Å / Origin y: -8.5447 Å / Origin z: -5.307 Å
111213212223313233
T0.1095 Å20.098 Å20.0861 Å2--0.1608 Å2-0.0538 Å2---0.1194 Å2
L4.8983 °21.9923 °20.7923 °2-8.2179 °20.5414 °2--9.4206 °2
S0.0124 Å °-0.038 Å °0.3661 Å °-0.2066 Å °0.0335 Å °-0.2201 Å °-0.4965 Å °0.2602 Å °-0.0458 Å °
Refinement TLS groupSelection details: { A|* }

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