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- PDB-9q39: Structure of a sortase-linked cytochrome c peroxidase - cytochrom... -

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Basic information

Entry
Database: PDB / ID: 9q39
TitleStructure of a sortase-linked cytochrome c peroxidase - cytochrome c fusion protein
ComponentsPeroxidase,Cytochrome c isoform 1
KeywordsOXIDOREDUCTASE / Peroxidase / Electron Transfer / Disordered Linkers
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase activity / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / hydrogen peroxide catabolic process ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase activity / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / hydrogen peroxide catabolic process / response to reactive oxygen species / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Peroxidase / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsClark, J.C. / Zawistowski, R.K. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2129728 United States
CitationJournal: To Be Published
Title: Structure of a sortase-linked cytochrome c peroxidase - cytochrome c fusion protein
Authors: Zawistowski, R.K. / Clark, J.C. / Crane, B.R.
History
DepositionAug 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxidase,Cytochrome c isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5754
Polymers46,2451
Non-polymers1,3303
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.658, 46.409, 60.604
Angle α, β, γ (deg.)90.000, 107.397, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 46244.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCRG_04081, CYC1, YJR048W, J1653 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3LRE1, UniProt: P00044, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Upon purification, CcP-GGSG(2x)LPATGGG was buffer exchanged into filtered nanopure water and concentrated to 0.5 mM. Initial crystal hits were obtained using a Gryphon robot (Arts Robbins ...Details: Upon purification, CcP-GGSG(2x)LPATGGG was buffer exchanged into filtered nanopure water and concentrated to 0.5 mM. Initial crystal hits were obtained using a Gryphon robot (Arts Robbins Instrument). Larger crystals were optimized via vapor diffusion in 4 microliter sitting drops, which were mixed 1:1 with well solution (14-20 % PEG 8000, 40 mM KH2PO4, 20 % glycerol, pH 3.0-5.5). Crystals growing under these conditions formed within a week.
PH range: 3.0 - 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.24→44.42 Å / Num. obs: 6454 / % possible obs: 94.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 61.64 Å2 / CC1/2: 0.967 / CC star: 0.992 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.179 / Rrim(I) all: 0.315 / Net I/σ(I): 4.4
Reflection shellResolution: 3.24→3.49 Å / Rmerge(I) obs: 0.626 / Num. unique obs: 1337 / CC1/2: 0.679 / CC star: 0.899 / Rpim(I) all: 0.434 / Rrim(I) all: 0.766 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
RAPDdata reduction
RAPDdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→44.42 Å / SU ML: 0.5246 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.4548
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3313 650 10.12 %
Rwork0.2759 5772 -
obs0.2817 6422 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.66 Å2
Refinement stepCycle: LAST / Resolution: 3.24→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 91 0 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353453
X-RAY DIFFRACTIONf_angle_d0.734694
X-RAY DIFFRACTIONf_chiral_restr0.0393457
X-RAY DIFFRACTIONf_plane_restr0.0046609
X-RAY DIFFRACTIONf_dihedral_angle_d14.56781252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.490.39261260.32541157X-RAY DIFFRACTION94.13
3.49-3.840.38211340.30321155X-RAY DIFFRACTION92.93
3.84-4.40.32851290.26211166X-RAY DIFFRACTION93.64
4.4-5.540.31721330.27211147X-RAY DIFFRACTION91.36
5.54-44.420.28841280.25041147X-RAY DIFFRACTION88.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.04319627488-0.06702128286281.13111682240.686477796720.7358352551992.841529281720.1195369751890.300805035087-0.147717486786-0.203887690714-0.04556742498190.08733954584770.0407626553160.166252524376-0.04650903685450.475637391696-0.0078336887195-0.2240278454780.289614382780.05268269736490.523119050162-26.8915449926-26.229296654412.4864175051
22.396608022921.015738641040.4091990928283.22766150.5434129191220.135258209923-0.311887434937-0.9264309764670.6832470941331.82035424962-0.120623761091-0.786945906566-0.8596727094280.2779239528520.4674295279681.07138126585-0.10195880598-0.4528082986990.927841737005-0.05806120588090.874169318707-27.5547934914-12.32074786240.1026023051
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 296 )1 - 2961 - 296
22chain 'A' and (resid 311 through 413 )311 - 413311 - 413

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