9FBA | pdb_00009fba

Dye-decolourising peroxidase DtpB (392 kGy)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.273 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.244 (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

Dye-decolourising peroxidase DtpB (392 kGy)

Lucic, M.Worrall, J.A.R.Hough, M.A.Strange, R.W.Owen, R.L.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
A, B, C, D, E
A, B, C, D, E, F
313Streptomyces lividans 1326Mutation(s): 0 
Gene Names: SLI_7409
UniProt
Find proteins for A0A7U9HFU5 (Streptomyces lividans 1326)
Explore A0A7U9HFU5 
Go to UniProtKB:  A0A7U9HFU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U9HFU5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
I [auth C]
J [auth D]
L [auth E]
G [auth A],
H [auth B],
I [auth C],
J [auth D],
L [auth E],
M [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PG4
Query on PG4

Download Ideal Coordinates CCD File 
K [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.273 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.965α = 90
b = 121.963β = 90
c = 199.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release