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- PDB-7mri: Crystal structure of N63T yeast iso-1-cytochrome c -

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Basic information

Entry
Database: PDB / ID: 7mri
TitleCrystal structure of N63T yeast iso-1-cytochrome c
ComponentsCytochrome c isoform 1
KeywordsELECTRON TRANSPORT / Peroxidase activity / electron transport chain
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
HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsLei, H. / Bowler, B.E. / Evenson, G.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1904895 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: Effect on intrinsic peroxidase activity of substituting coevolved residues from Omega-loop C of human cytochrome c into yeast iso-1-cytochrome c.
Authors: Frederick, A.K. / Thompson, S.L. / Vakharia, Z.M. / Cherney, M.M. / Lei, H. / Evenson, G. / Bowler, B.E.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c isoform 1
C: Cytochrome c isoform 1
E: Cytochrome c isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6876
Polymers35,8313
Non-polymers1,8563
Water1,65792
1
A: Cytochrome c isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5622
Polymers11,9441
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cytochrome c isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5622
Polymers11,9441
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cytochrome c isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5622
Polymers11,9441
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.250, 59.250, 92.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: -3 - 103 / Label seq-ID: 2 - 107

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CB
12AA
22EC
13CB
23EC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cytochrome c isoform 1 / Iso-1-cytochrome c / Cytochrome c aerobic isoform


Mass: 11943.666 Da / Num. of mol.: 3
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 (E. coli) / References: UniProt: P00044
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 30% w/v PEG1000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.46→41.93 Å / Num. obs: 11569 / % possible obs: 99.73 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.5
Reflection shellResolution: 2.46→2.52 Å / Rmerge(I) obs: 0.73 / Num. unique obs: 824

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YCC

2ycc


Resolution: 2.46→41.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.542 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.581 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 547 4.7 %RANDOM
Rwork0.1662 ---
obs0.1675 11022 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.93 Å2 / Biso mean: 33.069 Å2 / Biso min: 14.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å2-0 Å2-0 Å2
2--1.62 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: final / Resolution: 2.46→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 129 92 2738
Biso mean--20.95 32.39 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122733
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.7443687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44823.333117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9215489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.111159
X-RAY DIFFRACTIONr_chiral_restr0.1190.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022070
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A33480.09
12C33480.09
21A32660.11
22E32660.11
31C32660.12
32E32660.12
LS refinement shellResolution: 2.461→2.525 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 27 -
Rwork0.246 797 -
all-824 -
obs--100 %

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