8FJR | pdb_00008fjr

Structure of Thermomonospora curvata heme-containing DyP-type peroxidase E293H mutant

PDB DOI: https://doi.org/10.2210/pdb8FJR/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: 1.49 Å
R-Value Free:
0.176 (Depositor), 0.177 (DCC)
R-Value Work:
0.151 (Depositor), 0.153 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of Thermomonospora curvata heme-containing DyP-type peroxidase E293H mutant

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

To be published.

Macromolecule Content

Total Structure Weight: 88.61 kDa
Atom Count: 6,409
Modeled Residue Count: 720
Deposited Residue Count: 794
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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: 1.49 Å
R-Value Free: 0.176 (Depositor), 0.177 (DCC)
R-Value Work: 0.151 (Depositor), 0.153 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.345	α = 90
b = 92.02	β = 90
c = 97.466	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

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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

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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.