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- PDB-6rsi: cytochrome c co-crystallized with 25 eq. sulfonato-calix[8]arene ... -

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Basic information

Entry
Database: PDB / ID: 6rsi
Titlecytochrome c co-crystallized with 25 eq. sulfonato-calix[8]arene - structure 0
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / Molecular glues / Molecular switch / 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 / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,3137
Polymers12,0421
Non-polymers5,2716
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-24 kcal/mol
Surface area7740 Å2
Unit cell
Length a, b, c (Å)101.320, 101.320, 86.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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)
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-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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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 % 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, 2.20 M ammonium sulfate, 0.05 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: 0.98009 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: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.48→71.64 Å / Num. obs: 16406 / % possible obs: 100 % / Redundancy: 26.1 % / Biso Wilson estimate: 71.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.035 / Rrim(I) all: 0.176 / Net I/σ(I): 14.9
Reflection shellResolution: 2.482→2.525 Å / Rmerge(I) obs: 1.666 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 818 / CC1/2: 0.821 / Rpim(I) all: 0.334 / Rrim(I) all: 1.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→71.64 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.199 843 5.14 %RANDOM
Rwork0.194 ---
obs0.195 16406 100 %-
Displacement parametersBiso mean: 62.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.3461 Å20 Å20 Å2
2--2.3461 Å20 Å2
3----4.6923 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.48→71.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 343 134 1323
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011252HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.241779HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d406SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes2HARMONIC2
X-RAY DIFFRACTIONt_gen_planes180HARMONIC5
X-RAY DIFFRACTIONt_it1252HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion16.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion110SEMIHARMONIC5
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_contact1363SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.5 Å / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.341 -5.63 %
Rwork0.2211 369 -
all0.2265 391 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -31.3305 Å / Origin y: -5.7948 Å / Origin z: -0.2489 Å
111213212223313233
T-0.0459 Å20.0052 Å2-0.0148 Å2--0.0016 Å20.0165 Å2---0.0304 Å2
L2.4268 °2-1.0803 °20.3014 °2-2.5171 °2-0.5948 °2--2.1711 °2
S0.0058 Å °-0.0497 Å °0.0851 Å °0.094 Å °-0.0796 Å °-0.097 Å °-0.0934 Å °0.0988 Å °0.0737 Å °
Refinement TLS groupSelection details: { A|* }

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