8FJQ | pdb_00008fjq

Structure of Thermomonospora curvata heme-containing DyP-type peroxidase E293G mutant

PDB DOI: https://doi.org/10.2210/pdb8FJQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermomonospora curvata
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-12-20 Released: 2023-11-29
Deposition Author(s): Khadka, S., Li, P., Geisbrecht, B.V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.173 (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

Structure of Thermomonospora curvata heme-containing DyP-type peroxidase E293G mutant

Khadka, S., Geisbrecht, B., Li, P.

To be published.

Macromolecule Content

Total Structure Weight: 88.44 kDa
Atom Count: 6,118
Modeled Residue Count: 721
Deposited Residue Count: 794
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dyp-type peroxidase	A, B	397	Thermomonospora curvata	Mutation(s): 1 Gene Names: Tcur_2987
UniProt
Find proteins for D1A807 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1A807 Go to UniProtKB: D1A807
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D1A807
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM 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: 1.62 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.632	α = 90
b = 92.405	β = 90
c = 97.259	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Geisbrecht, B.V.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM140852

Revision History (Full details and data files)

Version 1.0: 2023-11-29
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.