8OLH

Y345F Variant of Dye Type Peroxidase Aa (DtpAa) from Streptomyces lividans

PDB DOI: https://doi.org/10.2210/pdb8OLH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces lividans 1326
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2023-03-30 Released: 2024-04-10
Deposition Author(s): Lucic, M., Worrall, J.A.R., Hough, M.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free: 0.159
R-Value Work: 0.133
R-Value Observed: 0.134

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

Y345F Variant of Dye Type Peroxidase Aa (DtpAa) from Streptomyces lividans

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

To be published.

Macromolecule Content

Total Structure Weight: 89.7 kDa
Atom Count: 6,689
Modelled Residue Count: 725
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

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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free: 0.159
R-Value Work: 0.133
R-Value Observed: 0.134
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.022	α = 90
b = 67.788	β = 105.66
c = 73.024	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-10

Deposition Author(s):

Worrall, J.A.R.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-04-10
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.