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- PDB-6gd7: Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG -

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Basic information

Entry
Database: PDB / ID: 6gd7
TitleCytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG
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 / 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 / molecular replacement / Resolution: 1.55 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: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Auto-regulated Protein Assembly on a Supramolecular Scaffold.
Authors: Rennie, M.L. / Fox, G.C. / Perez, J. / Crowley, P.B.
History
DepositionApr 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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
Revision 1.3Oct 23, 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)14,2424
Polymers12,0421
Non-polymers2,2003
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-25 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.420, 81.420, 82.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#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
#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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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

CrystalDescription: Large red/pink rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5 % PEG 3350 (2x protein solution : 1x crystallisation condition)

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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: 1.55→40.71 Å / Num. obs: 29520 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 1 / Rpim(I) all: 0.026 / Rrim(I) all: 0.056 / Net I/σ(I): 12.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.9 % / Num. unique obs: 1434 / CC1/2: 0.49 / Rpim(I) all: 0.256 / Rrim(I) all: 0.516 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LYC chain A

5lyc


Resolution: 1.55→40.71 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.896 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 1501 5.1 %RANDOM
Rwork0.1493 ---
obs0.151 28013 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.01 Å2 / Biso mean: 30.532 Å2 / Biso min: 15.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 1.55→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 145 177 1168
Biso mean--29.08 46.12 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191116
X-RAY DIFFRACTIONr_bond_other_d0.0020.02987
X-RAY DIFFRACTIONr_angle_refined_deg1.4372.1391551
X-RAY DIFFRACTIONr_angle_other_deg0.9733.0022314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40424.76242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81515194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.262154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021217
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02223
X-RAY DIFFRACTIONr_rigid_bond_restr1.60432092
X-RAY DIFFRACTIONr_sphericity_bonded7.76752045
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 99 -
Rwork0.345 2070 -
all-2169 -
obs--99.95 %

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