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- PDB-5t7h: Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6 -

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Basic information

Entry
Database: PDB / ID: 5t7h
TitleCrystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / cytochrome C / peroxidase activity / CYMAL6
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / 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 / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / 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
HEME C / 6-cyclohexylhexan-1-ol / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsMcclelland, L. / Mou, T.C. / Sprang, S.R. / Bowler, B.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM10003546 United States
National Science Foundation (NSF, United States)CHE-0910616 United States
National Science Foundation (NSF, United States)CHE-1306903 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons.
Authors: McClelland, L.J. / Steele, H.B. / Whitby, F.G. / Mou, T.C. / Holley, D. / Ross, J.B. / Sprang, S.R. / Bowler, B.E.
History
DepositionSep 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_comp_id_2 / _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_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
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)52,59921
Polymers48,5234
Non-polymers4,07617
Water5,765320
1
A: Cytochrome c iso-1
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,25210
Polymers24,2622
Non-polymers1,9908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-156 kcal/mol
Surface area11310 Å2
MethodPISA
2
B: Cytochrome c iso-1
C: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,34811
Polymers24,2622
Non-polymers2,0869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-147 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.351, 56.122, 56.127
Angle α, β, γ (deg.)75.65, 63.37, 63.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome c iso-1


Mass: 12130.861 Da / Num. of mol.: 4 / Mutation: K72A, C10S
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 / Plasmid: PRBS_BTR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00044
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZE7 / 6-cyclohexylhexan-1-ol


Mass: 184.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O
#4: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 75% (NH4)2SO4, AN 86% (NH4)2SO4 AND 0.1 M TRIS RESERVOIR SOLUTION, AND 5.6 MM CYMAL-6., PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 21, 2015
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.003→27.15 Å / Num. obs: 31532 / % possible obs: 95.8 % / Redundancy: 1.7 % / Biso Wilson estimate: 30.42 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 11.9
Reflection shellResolution: 2.003→2.08 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.26 / % possible all: 90.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXphasing
PHENIX1.9_1692refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MU8

4mu8


Resolution: 2.003→7.98 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98
RfactorNum. reflection% reflection
Rfree0.248 1964 6.32 %
Rwork0.198 --
obs0.202 31066 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 269 320 3893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123772
X-RAY DIFFRACTIONf_angle_d1.2325102
X-RAY DIFFRACTIONf_dihedral_angle_d15.7051344
X-RAY DIFFRACTIONf_chiral_restr0.044508
X-RAY DIFFRACTIONf_plane_restr0.005604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0033-2.05250.38271140.27651873X-RAY DIFFRACTION88
2.0525-2.1070.2731450.26312095X-RAY DIFFRACTION95
2.107-2.16780.38351360.25292084X-RAY DIFFRACTION96
2.1678-2.23630.33961430.25062093X-RAY DIFFRACTION97
2.2363-2.31440.34831590.23972012X-RAY DIFFRACTION95
2.3144-2.40460.27471530.22292109X-RAY DIFFRACTION97
2.4046-2.51080.29241420.20442125X-RAY DIFFRACTION97
2.5108-2.63860.25131480.19982097X-RAY DIFFRACTION98
2.6386-2.79720.21491320.20372149X-RAY DIFFRACTION97
2.7972-3.00250.26071420.19972089X-RAY DIFFRACTION97
3.0025-3.28530.25651350.20622154X-RAY DIFFRACTION97
3.2853-3.7180.23431370.18892089X-RAY DIFFRACTION97
3.718-4.53620.21631330.16152091X-RAY DIFFRACTION96
4.5362-7.97880.18991450.17362042X-RAY DIFFRACTION94

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