9Q39 | pdb_00009q39

Structure of a sortase-linked cytochrome c peroxidase - cytochrome c fusion protein

PDB DOI: https://doi.org/10.2210/pdb9Q39/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-18 Released: 2026-03-11
Deposition Author(s): Clark, J.C., Zawistowski, R.K., Crane, B.R.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free:
0.331 (Depositor), 0.330 (DCC)
R-Value Work:
0.276 (Depositor), 0.275 (DCC)
R-Value Observed:
0.282 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Structure of a sortase-linked cytochrome c peroxidase - cytochrome c fusion protein

Zawistowski, R.K., Clark, J.C., Crane, B.R.

To be published.

Macromolecule Content

Total Structure Weight: 47.57 kDa
Atom Count: 3,354
Modeled Residue Count: 413
Deposited Residue Count: 413
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxidase,Cytochrome c isoform 1	A	413	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SCRG_04081, CYC1, YJR048W, J1653 EC: 1.11.1 (PDB Primary Data), 1.11.1.5 (UniProt)
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044 Go to UniProtKB: P00044
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431 Go to UniProtKB: P00431
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P00044 P00431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free: 0.331 (Depositor), 0.330 (DCC)
R-Value Work: 0.276 (Depositor), 0.275 (DCC)
R-Value Observed: 0.282 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.658	α = 90
b = 46.409	β = 107.397
c = 60.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
RAPD	data reduction
RAPD	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-11

Deposition Author(s):

Zawistowski, R.K.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2129728

Revision History (Full details and data files)

Version 1.0: 2026-03-11
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.