4GS1 | pdb_00004gs1

Crystal structure of DyP-type peroxidase from Thermobifida cellulosilytica

• PDB DOI: https://doi.org/10.2210/pdb4GS1/pdb

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


• Deposited: 2012-08-27 Released: 2013-09-11 
• Deposition Author(s): Lukk, T., Hetta, A.M.A., Jones, A., Solbiati, J., Majumdar, S., Cronan, J.E., Gerlt, J.A., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

DyP-type peroxidases from Stretptomyces and Thermobifida can modify organosolv lignin.

Lukk, T., Hetta, A.M.A., Jones, A., Solbiati, J., Majumdar, S., Cronan, J.E., Gerlt, J.A., Nair, S.K.

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)

Macromolecule Content 

• Total Structure Weight: 86.4 kDa 
• Atom Count: 6,778 
• Modeled Residue Count: 751 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DyP-type peroxidase	A, B	395	Thermobifida cellulosilytica	Mutation(s): 0  EC: 1.11.1.19
UniProt
Find proteins for U3KRF5 (Thermobifida cellulosilytica) Explore U3KRF5  Go to UniProtKB:  U3KRF5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXY	D [auth A], G [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.68	α = 90
b = 91.19	β = 90
c = 110.55	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Lukk, T., Hetta, A.M.A., Jones, A., Solbiati, J., Majumdar, S., Cronan, J.E., Gerlt, J.A., Nair, S.K.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description