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- PDB-6y0j: Cytochrome c in complex with phosphonato-calix[6]arene and sulfon... -

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Basic information

Entry
Database: PDB / ID: 6y0j
TitleCytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / Molecular glue / calixarene / protein assembly / framework / supramolecular chemistry
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
phosphonato-calix[6]arene / sulfonato-calix[8]arene / HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsEngilberge, S. / Rennie, M.L. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: Supramolecular Chemistry / Year: 2021
Title: Protein-macrocycle framework engineering: supramolecular copolymerisation with two disparate calixarenes
Authors: Mockler, N.M. / Engilberge, S. / Rennie, M.L. / Raston, C.L. / Crowley, P.B.
History
DepositionFeb 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c iso-1
B: Cytochrome c iso-1
C: Cytochrome c iso-1
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,08614
Polymers48,1674
Non-polymers9,91910
Water1,71195
1
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6602
Polymers12,0421
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3835
Polymers12,0421
Non-polymers4,3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2664
Polymers12,0421
Non-polymers3,2253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7773
Polymers12,0421
Non-polymers1,7352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.573, 67.573, 373.866
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Cytochrome c iso-1


Mass: 12041.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-7AZ / phosphonato-calix[6]arene


Mass: 1116.611 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H42O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.12 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 10 % PEG 8000, 8 % ethylene glycol, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98008 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 2.7→62.31 Å / Num. obs: 16206 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 56.24 Å2 / CC1/2: 0.939 / Rmerge(I) obs: 0.704 / Rpim(I) all: 0.163 / Net I/σ(I): 5.3
Reflection shellResolution: 2.7→3.05 Å / Num. unique obs: 810 / CC1/2: 0.097 / Rpim(I) all: 0.592

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TYI

3tyi


Resolution: 2.7→62.31 Å / Cor.coef. Fo:Fc: 0.769 / Cor.coef. Fo:Fc free: 0.74 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.419
RfactorNum. reflection% reflectionSelection details
Rfree0.269 754 4.66 %RANDOM
Rwork0.245 ---
obs0.246 16167 61.5 %-
Displacement parametersBiso max: 147.5 Å2 / Biso mean: 60.16 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--5.2644 Å20 Å20 Å2
2---5.2644 Å20 Å2
3---10.5288 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: final / Resolution: 2.7→62.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 652 95 4094
Biso mean--63.52 22.35 -
Num. residues----427
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1345SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes673HARMONIC5
X-RAY DIFFRACTIONt_it4155HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion427SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4276SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4155HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5747HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion21.04
LS refinement shellResolution: 2.7→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3466 20 6.54 %
Rwork0.2188 286 -
all0.2275 306 -
obs--6.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0151-0.28712.6981-0.65573.40086.25590.1786-0.0288-0.1347-0.311-0.1781-0.20640.2764-0.0963-0.0004-1.38420.34020.04310.41960.40180.0135-19.4761-3.008537.2281
23.3952-2.3985-2.30695.3504-1.61635.68230.1409-0.32260.08210.0282-0.1011-0.0595-0.3549-0.0075-0.03980.05170.50290.1478-0.17370.16760.1309-12.474312.861810.1517
37.8027-2.14661.0263-5.0787-3.9376.37090.1308-0.1994-0.12980.0754-0.14860.2010.1468-0.08180.0179-1.73560.1215-0.11740.6233-0.1552-0.0383-46.3331-5.129851.6616
45.6575-1.25260.87994.46810.26229.62380.09110.0026-0.0127-0.2294-0.1012-0.04990.04820.18840.01010.07580.28970.03580.2248-0.10920.3945-51.1926-6.533916.8562
52.8814-1.0776-0.4497-0.68020.37860.26530.3416-0.03610.1245-0.4743-0.4335-0.07270.151-0.2860.0919-0.02630.23210.0785-0.0295-0.00580.071-25.17820.33275.8389
63.1636-0.92571.16752.0653-1.77651.43340.065-0.0622-0.0185-0.0621-0.1001-0.08140.028-0.09640.0351-0.17370.04220.09530.14270.0190.0149-33.07331.745444.731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-3 - 103
2X-RAY DIFFRACTION2{ B|* }B-3 - 103
3X-RAY DIFFRACTION3{ C|* }C-2 - 103
4X-RAY DIFFRACTION4{ D|* }D-3 - 103
5X-RAY DIFFRACTION5{ F|* }F202 - 204
6X-RAY DIFFRACTION6{ G|* }G1 - 2

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