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- PDB-5ncv: Crystal Structure of Cytochrome c in complex with p-Methylphospho... -

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Basic information

Entry
Database: PDB / ID: 5ncv
TitleCrystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / methylphosphonatocalix[4]arene / cytochrome c / lysine recognition / protein 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
p-Methylphosphonatocalix[4]arene / HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAlex, J.M. / Rennie, M.L. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Funding Ireland13/CDA/2168 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2018
Title: Phosphonated Calixarene as a ""Molecular Glue"" for Protein Crystallization
Authors: Alex, J.M. / Rennie, M.L. / Volpi, S. / Sansone, F. / Casnati, A. / Crowley, P.B.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 14, 2018Group: Data collection / 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.title
Revision 1.3Jan 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
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)27,7588
Polymers24,0842
Non-polymers3,6746
Water5,080282
1
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2975
Polymers12,0421
Non-polymers2,2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4613
Polymers12,0421
Non-polymers1,4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.917, 80.227, 47.807
Angle α, β, γ (deg.)90.000, 93.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c iso-1


Mass: 12041.770 Da / Num. of mol.: 2 / Mutation: T-5A, C102T
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 BL21(DE3) (bacteria) / 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-8TE / p-Methylphosphonatocalix[4]arene


Mass: 800.514 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H36O16P4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20 % PEG 8000, 50 mM NaCl, 50 mM sodium acetate (pH 5.6). [Cytochrome c] = 0.75 mM and [Methylphosphonatocalix[4]arene] = 0.3 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→47.74 Å / Num. obs: 34591 / % possible obs: 99.2 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.026 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3452 / Rpim(I) all: 0.158 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSOct15, 2015data reduction
XDSOct15, 2015data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YCC

1ycc


Resolution: 1.5→47.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.649 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 1707 4.9 %RANDOM
Rwork0.1704 ---
obs0.1719 32897 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.7 Å2 / Biso mean: 20.624 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-2.11 Å2
2---0.88 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: final / Resolution: 1.5→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1624 0 295 283 2202
Biso mean--22.19 33.06 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192110
X-RAY DIFFRACTIONr_bond_other_d0.0020.021853
X-RAY DIFFRACTIONr_angle_refined_deg1.6082.1522927
X-RAY DIFFRACTIONr_angle_other_deg1.0123.0024336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97824.86876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11715347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.671156
X-RAY DIFFRACTIONr_chiral_restr0.1220.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022292
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02420
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 118 -
Rwork0.242 2450 -
all-2568 -
obs--99.3 %

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