7RMU

Structure of Thermomonospora curvata heme-containing DyP-type peroxidase with a modified axial ligand

• PDB DOI: https://doi.org/10.2210/pdb7RMU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermomonospora curvata
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-28 Released: 2022-08-31 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

Structure of Thermomonospora curvata heme-containing DyP-type peroxidase with a modified axial ligand

Khadka, S., Geisbrecht, B., Li, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.98 kDa 
• Atom Count: 3,011 
• Modelled Residue Count: 361 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DyP-type Peroxidase	A	397	Thermomonospora curvata	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHS	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.698	α = 90
b = 87.698	β = 90
c = 107.87	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Khadka, S., Li, P., Geisbrecht, B.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM140852

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description