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- PDB-6gda: Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form... -

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Basic information

Entry
Database: PDB / ID: 6gda
TitleCytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / calixarene / scaffold / supramolecular / assembly
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / 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 ...Release of apoptotic factors from the mitochondria / Pyroptosis / 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
sulfonato-calix[8]arene / HEME C / SPERMINE / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsRennie, M.L. / Fox, G.C. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/ERC/B2912 and 13/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
DepositionApr 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 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

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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)18,39816
Polymers12,0421
Non-polymers6,35615
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-108 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.252, 101.252, 85.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Mutation: C102T, T-5A
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 BL21(DE3) (bacteria) / References: UniProt: P00044

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Non-polymers , 5 types, 24 molecules

#2: Chemical ChemComp-HEC / HEME C / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.1 M ammonium sulfate 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→85.31 Å / Num. obs: 11454 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.045 / Rrim(I) all: 0.131 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.8-2.958.50.66616320.4730.2430.71
8.85-85.317.30.0344370.9990.0130.037

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YCC

1ycc


Resolution: 2.8→71.7 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.126 / SU ML: 0.191 / SU R Cruickshank DPI: 0.2942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.236
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 570 5 %RANDOM
Rwork0.2219 ---
obs0.223 10844 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 175.25 Å2 / Biso mean: 68.516 Å2 / Biso min: 31.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---1.47 Å20 Å2
3---2.94 Å2
Refinement stepCycle: final / Resolution: 2.8→71.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 404 9 1259
Biso mean--90.23 48.69 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021290
X-RAY DIFFRACTIONr_bond_other_d0.0020.02990
X-RAY DIFFRACTIONr_angle_refined_deg1.1922.341821
X-RAY DIFFRACTIONr_angle_other_deg0.7143.0022295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1895107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91224.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42415163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.923153
X-RAY DIFFRACTIONr_chiral_restr0.0650.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021258
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02237
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 37 -
Rwork0.362 791 -
all-828 -
obs--100 %

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