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- PDB-5lft: Crystal structure of cytochrome c - Bromo-trisulfonatocalix[4]are... -

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Basic information

Entry
Database: PDB / ID: 5lft
TitleCrystal structure of cytochrome c - Bromo-trisulfonatocalix[4]arene complexes
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / cytochrome c / modified calixarene / bromo group
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / 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 / Respiratory electron transport / Detoxification of Reactive Oxygen Species / 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
Bromo-trisulfonatocalix[4]arene / BROMIDE ION / HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.249 Å
AuthorsDoolan, A.M. / Rennie, M.L. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/ERC/B2912 Ireland
CitationJournal: Chemistry / Year: 2018
Title: Protein Recognition by Functionalized Sulfonatocalix[4]arenes.
Authors: Doolan, A.M. / Rennie, M.L. / Crowley, P.B.
History
DepositionJul 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 10, 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
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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)15,0517
Polymers12,0421
Non-polymers3,0096
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-25 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.746, 38.045, 89.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

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Components

#1: Protein Cytochrome c iso-1 / Cytochrome c


Mass: 12041.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-6VB / Bromo-trisulfonatocalix[4]arene


Mass: 743.573 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H23BrO13S3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM NaOAc pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.249→44.825 Å / Num. obs: 33624 / % possible obs: 99.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 14.46 Å2 / Rsym value: 0.064 / Net I/av σ(I): 5.862 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.25-1.327.60.7730.9199.1
1.32-1.47.80.4641.61100
1.4-1.497.80.2682.71100
1.49-1.617.90.1564.71100
1.61-1.777.90.10371100
1.77-1.977.90.0827.91100
1.97-2.287.90.0669.51100
2.28-2.797.70.05511.41100
2.79-3.957.70.04513.7199.2
3.95-44.8256.30.04412.3187.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.35 Å44.83 Å
Translation1.35 Å44.83 Å

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tyi

3tyi


Resolution: 1.249→35.022 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2392 1707 5.09 %
Rwork0.2134 --
obs0.2148 33553 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.69 Å2 / Biso mean: 20.9639 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 1.249→35.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 180 194 1220
Biso mean--19.56 30.58 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011091
X-RAY DIFFRACTIONf_angle_d1.1091514
X-RAY DIFFRACTIONf_chiral_restr0.043134
X-RAY DIFFRACTIONf_plane_restr0.006172
X-RAY DIFFRACTIONf_dihedral_angle_d25.027388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2489-1.28560.31961370.34172595273298
1.2856-1.32710.31561240.312226152739100
1.3271-1.37460.2831410.281226302771100
1.3746-1.42960.2921380.274326292767100
1.4296-1.49470.29661390.253226572796100
1.4947-1.57350.23591470.240826452792100
1.5735-1.6720.25031360.234326492785100
1.672-1.80110.22151480.219426602808100
1.8011-1.98240.23781200.218227102830100
1.9824-2.26920.24721590.206226732832100
2.2692-2.85870.2331740.208326992873100
2.8587-35.03570.21971440.17962684282894

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