6UDG | pdb_00006udg

Crystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1

• PDB DOI: https://doi.org/10.2210/pdb6UDG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Elizabethkingia anophelis NUHP1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-09-19 Released: 2019-10-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.37 kDa 
• Atom Count: 4,557 
• Modeled Residue Count: 648 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol peroxidase	A, B, C, D	173	Elizabethkingia anophelis NUHP1	Mutation(s): 0  Gene Names: tpx, BD94_2659 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for A0A077EJK0 (Elizabethkingia anophelis NUHP1) Explore A0A077EJK0  Go to UniProtKB:  A0A077EJK0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36udg

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.59	α = 90
b = 107.8	β = 90
c = 113.7	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary