8PXQ

SFX Ferric structure of Y389F variant of A type dye-decolourising peroxidase DtpAa

PDB DOI: https://doi.org/10.2210/pdb8PXQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces lividans 1326
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-07-24 Released: 2025-02-12
Deposition Author(s): Lucic, M., Worrall, J.A.R., Hough, M.A., Pfalzgraf, H.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.205 (Depositor), 0.212 (DCC)
R-Value Work:
0.167 (Depositor), 0.177 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

SFX ferric structure of A type dye-decolourising peroxidase DtpAa

Lucic, M., Thompson, A., Worrall, J.A.R., Hough, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 89.7 kDa
Atom Count: 5,952
Modelled Residue Count: 724
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deferrochelatase	A, B	417	Streptomyces lividans 1326	Mutation(s): 1 Gene Names: SLI_2602 EC: 1.11.1
UniProt
Find proteins for A0A7U9DT46 (Streptomyces lividans 1326) Explore A0A7U9DT46 Go to UniProtKB: A0A7U9DT46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7U9DT46
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.205 (Depositor), 0.212 (DCC)
R-Value Work: 0.167 (Depositor), 0.177 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.567	α = 90
b = 68.14	β = 105.5
c = 74.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Worrall, J.A.R.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R021015/1

Revision History (Full details and data files)

Version 1.0: 2025-02-12
Type: Initial release

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.