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- PDB-4mu8: Crystal structure of an oxidized form of yeast iso-1-cytochrome c... -

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Basic information

Entry
Database: PDB / ID: 4mu8
TitleCrystal structure of an oxidized form of yeast iso-1-cytochrome c at pH 8.8
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / oxidized form at pH 8.8 / All alpha proteins / cytochrome C / electron carrier / Peroxidase Activity / HEME Binding / mitochondria
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-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / TERTIARY-BUTYL ALCOHOL / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMcClelland, L.J. / Mou, T.-C. / Jeakins-Cooley, M.E. / Sprang, S.R. / Bowler, B.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of a mitochondrial cytochrome c conformer competent for peroxidase activity.
Authors: McClelland, L.J. / Mou, T.C. / Jeakins-Cooley, M.E. / Sprang, S.R. / Bowler, B.E.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_struct_special_symmetry / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _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 / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)26,31916
Polymers23,9992
Non-polymers2,32014
Water6,630368
1
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0777
Polymers12,0001
Non-polymers1,0776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2439
Polymers12,0001
Non-polymers1,2438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.621, 93.621, 155.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-203-

SO4

21A-206-

TBU

31A-206-

TBU

41B-203-

SO4

51B-207-

TBU

61B-207-

TBU

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome c iso-1


Mass: 11999.667 Da / Num. of mol.: 2 / Mutation: K78A, C108S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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

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Non-polymers , 5 types, 382 molecules

#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 4.09 Å3/Da / Density % sol: 69.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 90% ammonia sulfate, 0.1 M Tris-HCl (pH 8.8), 4% tert-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2013 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal [Si(111)]; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→15 Å / Num. obs: 71415 / % possible obs: 99.89 % / Observed criterion σ(I): 3 / Redundancy: 9 % / Biso Wilson estimate: 15.42 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.16
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.43 / Num. unique all: 3497 / Rsym value: 0.843 / % possible all: 99.23

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YCC

2ycc


Resolution: 1.45→7.998 Å / SU ML: 0.11 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): -2 / Phase error: 15.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1538 1988 2.8 %RANDOM
Rwork0.1452 ---
obs0.1455 70956 99.93 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 1.45→7.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 147 368 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191935
X-RAY DIFFRACTIONf_angle_d1.5442632
X-RAY DIFFRACTIONf_dihedral_angle_d20.643717
X-RAY DIFFRACTIONf_chiral_restr0.255250
X-RAY DIFFRACTIONf_plane_restr0.007309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.45-1.4860.26941400.253948514851
1.486-1.5260.27441390.230147964796
1.526-1.57050.23471400.205448644864
1.5705-1.62080.15531400.175148704870
1.6208-1.67820.17331400.164848554855
1.6782-1.74480.15011400.145748734873
1.7448-1.82330.15871410.144749004900
1.8233-1.91820.15851420.137148874887
1.9182-2.03650.13081410.133949264926
2.0365-2.19070.16631410.134549164916
2.1907-2.40570.15481430.139249464946
2.4057-2.74150.14081440.132649894989
2.7415-3.40890.1551450.137650505050
3.4089-7.99840.12781520.137452455245

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