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- PDB-5kpf: Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]ar... -

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Basic information

Entry
Database: PDB / ID: 5kpf
TitleCrystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / cytochrome c / modified calixarene / phenyl group
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
Phenyl-trisulfonatocalix[4]arene / HEME C / NITRATE ION / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.698 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 1.2Jan 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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1236
Polymers24,0842
Non-polymers2,0404
Water4,774265
1
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7223
Polymers12,0421
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4013
Polymers12,0421
Non-polymers1,3592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.417, 61.085, 173.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

21B-423-

HOH

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Components

#1: Protein Cytochrome c iso-1


Mass: 12041.770 Da / Num. of mol.: 2
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 / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-6VJ / Phenyl-trisulfonatocalix[4]arene


Mass: 740.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H28O13S3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20 mM PEG 3350, 200 mM Ammonium Nitrate pH 6.3 cyt c-sclx4 seed (grown in 18% 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: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.698→86.701 Å / Num. all: 20722 / Num. obs: 20722 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 16.89 Å2 / Rpim(I) all: 0.057 / Rrim(I) all: 0.152 / Rsym value: 0.14 / Net I/av σ(I): 4.371 / Net I/σ(I): 9.1 / Num. measured all: 145765
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.796.81.2140.61965329060.4991.3151.2141.598.1
1.79-1.97.20.7071.12022328260.2840.7620.7072.7100
1.9-2.037.10.4711.51906326730.190.5090.4714.2100
2.03-2.197.10.2662.71784624990.1070.2870.2666.6100
2.19-2.47.20.1873.91627322680.0750.2010.1878.5100
2.4-2.697.20.1335.31505421050.0530.1440.13310.9100
2.69-3.17.10.09771308518490.0390.1040.09714.7100
3.1-3.86.90.0748.21095815880.0310.080.07420.3100
3.8-5.3770.0619.1875712550.0250.0660.06124.6100
5.37-43.3516.40.0589.548537530.0250.0630.0582299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å43.35 Å
Translation1.7 Å43.35 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tyi
Resolution: 1.698→43.351 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1099 5.32 %
Rwork0.1578 19561 -
obs0.1604 20660 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.23 Å2 / Biso mean: 20.1775 Å2 / Biso min: 8.74 Å2
Refinement stepCycle: final / Resolution: 1.698→43.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 140 265 2096
Biso mean--15.86 29 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011921
X-RAY DIFFRACTIONf_angle_d1.1272607
X-RAY DIFFRACTIONf_chiral_restr0.051245
X-RAY DIFFRACTIONf_plane_restr0.004321
X-RAY DIFFRACTIONf_dihedral_angle_d16.603705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6984-1.77570.29081350.25252327246297
1.7757-1.86930.27681340.209224272561100
1.8693-1.98640.23551350.17924162551100
1.9864-2.13980.22961540.169624052559100
2.1398-2.35510.23341190.159824622581100
2.3551-2.69590.2191530.157424422595100
2.6959-3.39630.19771310.145924772608100
3.3963-43.36490.15861380.133626052743100

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