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- PDB-6rsj: Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene ... -

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Basic information

Entry
Database: PDB / ID: 6rsj
TitleCytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene and soaked with 25 eq. spermine - structure I
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / Molecular glues / Molecular switch / spermine / polyamine / calixarene / supramolecular chemistry / cytc
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
sulfonato-calix[8]arene / HEME C / SPERMINE / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsEngilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: Acs Nano / Year: 2019
Title: Tuning Protein Frameworks via Auxiliary Supramolecular Interactions.
Authors: Engilberge, S. / Rennie, M.L. / Dumont, E. / Crowley, P.B.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,18614
Polymers12,0421
Non-polymers6,14413
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-42 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.452, 101.452, 85.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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 S288c (yeast) / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044

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Non-polymers , 6 types, 159 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

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 % sol: 85 % / Description: red diamond
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.10 M HEPES pH 7.5, 0.15 M NaCl, 2.2 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98008 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 2.268→71.737 Å / Num. obs: 21272 / % possible obs: 100 % / Redundancy: 26.5 % / Biso Wilson estimate: 62.11 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.019 / Net I/σ(I): 25.7
Reflection shellResolution: 2.268→2.307 Å / Rmerge(I) obs: 1.801 / Num. unique obs: 1050 / Rpim(I) all: 0.346

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GD9

6gd9


Resolution: 2.27→54.99 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1061 4.99 %RANDOM
Rwork0.193 ---
obs0.194 21271 100 %-
Displacement parametersBiso mean: 59.75 Å2
Baniso -1Baniso -2Baniso -3
1-3.6815 Å20 Å20 Å2
2--3.6815 Å20 Å2
3----7.363 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.27→54.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 399 149 1394
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011304HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.161827HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d438SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes2HARMONIC2
X-RAY DIFFRACTIONt_gen_planes176HARMONIC5
X-RAY DIFFRACTIONt_it1304HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion16.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion109SEMIHARMONIC5
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_contact1427SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.28 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2713 -5.87 %
Rwork0.2057 401 -
all0.2091 426 -
obs--98.6 %
Refinement TLS params.Method: refined / Origin x: 31.3073 Å / Origin y: -5.5822 Å / Origin z: -21.3031 Å
111213212223313233
T-0.0479 Å2-0.0075 Å2-0.0075 Å2--0.0074 Å2-0.0331 Å2---0.0318 Å2
L1.8569 °20.8848 °20.334 °2-1.9969 °20.1609 °2--1.5121 °2
S-0.0159 Å °0.015 Å °0.0752 Å °-0.0451 Å °-0.0399 Å °0.0817 Å °-0.0633 Å °-0.0589 Å °0.0559 Å °
Refinement TLS groupSelection details: { A|* }

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