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- PDB-7pr4: Cocrystal Form II of a cytochrome c, sulfonato-thiacalix[4]arene ... -

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Basic information

Entry
Database: PDB / ID: 7pr4
TitleCocrystal Form II of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / calixarene / molecular glue / synthetic receptor / alpha helix / thiacalixarene / metal cluster
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-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
sulfonato-thiacalix[4]arene / HEME C / PHOSPHATE ION / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsFlood, R.J. / Ramberg, K. / Guagnini, F. / Crowley, P.B.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
Science Foundation Ireland13/CDA/2168 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2022
Title: Protein Frameworks with Thiacalixarene and Zinc.
Authors: Flood, R.J. / Ramberg, K.O. / Mengel, D.B. / Guagnini, F. / Crowley, P.B.
History
DepositionSep 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,15512
Polymers12,0421
Non-polymers2,11311
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-238 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.624, 36.106, 82.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044

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Non-polymers , 5 types, 164 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-80M / sulfonato-thiacalix[4]arene


Mass: 816.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H16O16S8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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 Matthews: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 3350, 100 mM sodium acetate pH 5.6, 10 mM zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→41.45 Å / Num. obs: 26001 / % possible obs: 99.6 % / Redundancy: 10.6 % / CC1/2: 0.984 / Rpim(I) all: 0.065 / Rrim(I) all: 0.217 / Net I/σ(I): 13.3
Reflection shellResolution: 1.3→1.3 Å / Num. unique obs: 1216 / CC1/2: 0.798 / Rpim(I) all: 0.418 / Rrim(I) all: 0.881

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LYC

5lyc


Resolution: 1.32→41.45 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1306 5.03 %
Rwork0.1868 24648 -
obs0.1887 25954 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.39 Å2 / Biso mean: 16.2965 Å2 / Biso min: 7.2 Å2
Refinement stepCycle: final / Resolution: 1.32→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 112 153 1106
Biso mean--14.43 30.05 -
Num. residues----107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.32-1.370.32841460.29772616276297
1.37-1.430.31661480.25192669281799
1.43-1.510.24121570.198527102867100
1.51-1.60.22461280.174427092837100
1.6-1.720.17021400.162227342874100
1.72-1.90.24451240.164527542878100
1.9-2.170.20651720.168627192891100
2.17-2.740.19691420.181228112953100
2.74-41.450.2311490.1929263075100

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