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- PDB-6gd9: Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form -

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Basic information

Entry
Database: PDB / ID: 6gd9
TitleCytochrome c in complex with Sulfonato-calix[8]arene, P43212 form
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / calixarene / scaffold / supramolecular / assembly
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / 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 ...Pyroptosis / Release of apoptotic factors from the mitochondria / 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 / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,37012
Polymers12,0421
Non-polymers6,32811
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-27 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.590, 101.590, 86.520
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, 46 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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

CrystalDescription: Small pink/red crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.85 M ammonium sulfate 0.1 M HEPES pH 7.0 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: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.98 Å
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→71.83 Å / Num. obs: 13680 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.988 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.054 / Rrim(I) all: 0.175 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.65-2.7810.10.50717860.5070.1660.535100
8.79-71.839.30.0794450.9930.0280.08499.9

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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: 1YCC

1ycc


Resolution: 2.65→71.83 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.815 / SU B: 9.712 / SU ML: 0.194 / SU R Cruickshank DPI: 0.2708 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.246
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 688 5 %RANDOM
Rwork0.2426 ---
obs0.2447 12959 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.92 Å2 / Biso mean: 47.769 Å2 / Biso min: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---1.47 Å20 Å2
3---2.94 Å2
Refinement stepCycle: final / Resolution: 2.65→71.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 436 35 1317
Biso mean--67.83 34.56 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021330
X-RAY DIFFRACTIONr_bond_other_d0.0010.021034
X-RAY DIFFRACTIONr_angle_refined_deg1.1822.3611881
X-RAY DIFFRACTIONr_angle_other_deg0.7083.0022415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48724.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.984153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021258
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02237
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 53 -
Rwork0.371 933 -
all-986 -
obs--100 %

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