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- PDB-6gd8: Cytochrome c in complex with Sulfonato-calix[8]arene, P31 form -

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Basic information

Entry
Database: PDB / ID: 6gd8
TitleCytochrome c in complex with Sulfonato-calix[8]arene, P31 form
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 / 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
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: 2.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)56,59912
Polymers48,1674
Non-polymers8,4328
Water73941
1
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6394
Polymers12,0421
Non-polymers3,5973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1503
Polymers12,0421
Non-polymers2,1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1503
Polymers12,0421
Non-polymers2,1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 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
Unit cell
Length a, b, c (Å)66.680, 66.680, 142.881
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: -5 - 103 / Label seq-ID: 1 - 108

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cytochrome c iso-1


Mass: 12041.770 Da / Num. of mol.: 4 / 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 / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.69 % / Description: Small pink-red rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24 % PEG 3350 0.27 M NaCl 0.09 M MES pH 5.5 (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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.169
11-K, -H, -L20.332
11-h,-k,l30.332
11K, H, -L40.167
ReflectionResolution: 2.5→71.44 Å / Num. obs: 24569 / % possible obs: 99.7 % / Redundancy: 3.1 % / CC1/2: 0.984 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.086 / Rrim(I) all: 0.158 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.60.3927590.6070.2590.4799.9
9.01-71.440.0565360.9920.0360.06799.7

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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: 2.5→57.75 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.403 / SU ML: 0.105 / SU R Cruickshank DPI: 0.0675 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1090 4.4 %RANDOM
Rwork0.1761 ---
obs0.1772 23441 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.5 Å2 / Biso mean: 41.858 Å2 / Biso min: 2.72 Å2
Baniso -1Baniso -2Baniso -3
1-13.98 Å20 Å20 Å2
2--13.98 Å20 Å2
3----27.96 Å2
Refinement stepCycle: final / Resolution: 2.5→57.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 497 41 3922
Biso mean--42.32 25.37 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194015
X-RAY DIFFRACTIONr_bond_other_d0.0020.023476
X-RAY DIFFRACTIONr_angle_refined_deg1.3752.1295522
X-RAY DIFFRACTIONr_angle_other_deg0.9033.0028076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03424.595148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72815652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6131512
X-RAY DIFFRACTIONr_chiral_restr0.090.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024342
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02810
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A66840.07
12B66840.07
21A66440.07
22C66440.07
31A66640.06
32D66640.06
41B66180.08
42C66180.08
51B66180.08
52D66180.08
61C67180.05
62D67180.05
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 102 -
Rwork0.227 1764 -
all-1866 -
obs--99.84 %

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