4GT2

Crystal structure of DyP-type peroxidase (SCO3963) from Streptomyces coelicolor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein SCO3963A [auth B],
B [auth A],
C [auth E],
D [auth G]
465Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO3963
EC: 1.11.1.19 (PDB Primary Data), 1.11.1 (UniProt)
UniProt
Find proteins for Q9ZBW9 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9ZBW9 
Go to UniProtKB:  Q9ZBW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZBW9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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E [auth B],
J [auth A],
N [auth E],
S [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GOL
Query on GOL

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F [auth B]
I [auth B]
K [auth A]
M [auth A]
O [auth E]
F [auth B],
I [auth B],
K [auth A],
M [auth A],
O [auth E],
P [auth E],
R [auth E],
U [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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H [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
OXY
Query on OXY

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G [auth B],
L [auth A],
Q [auth E],
T [auth G]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.87α = 90
b = 203.2β = 110.73
c = 76.32γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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