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- PDB-6gd6: Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form wit... -

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Basic information

Entry
Database: PDB / ID: 6gd6
TitleCytochrome c in complex with Sulfonato-calix[8]arene, H3 form with ammonium sulfate
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: 1.2 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 16, 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)14,6308
Polymers12,0421
Non-polymers2,5887
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-66 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.003, 82.003, 82.535
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-412-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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, hanging drop
Details: 1.75 M ammonium sulfate 0.2 M NaCl (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: 1.2→35.68 Å / Num. obs: 64600 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.032 / Rrim(I) all: 0.064 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.223.30.53331860.7350.3410.63699.5
6.57-35.683.40.0383620.9770.0250.04691.9

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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: 5LYC chain A

5lyc


Resolution: 1.2→35.68 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.86 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1361 3238 5 %RANDOM
Rwork0.1189 ---
obs0.1197 61332 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.31 Å2 / Biso mean: 18.231 Å2 / Biso min: 9.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.2→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 164 294 1304
Biso mean--16.76 34.82 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021173
X-RAY DIFFRACTIONr_bond_other_d0.0010.021049
X-RAY DIFFRACTIONr_angle_refined_deg1.482.1521640
X-RAY DIFFRACTIONr_angle_other_deg0.8733.0022466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.40624.14641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77115212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.414155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021273
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02236
X-RAY DIFFRACTIONr_rigid_bond_restr0.96132222
X-RAY DIFFRACTIONr_sphericity_free24.7145243
X-RAY DIFFRACTIONr_sphericity_bonded8.36652223
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 230 -
Rwork0.274 4514 -
all-4744 -
obs--99.62 %

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