2J66 | pdb_00002j66

Structural characterisation of BtrK decarboxylase from butirosin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb2J66/pdb

• Classification: LYASE
• Organism(s): Niallia circulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-26 Released: 2006-09-28 
• Deposition Author(s): Popovic, B., Li, Y., Chirgadze, D.Y., Blundell, T.L., Spencer, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.213 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structural Characterisation of Btrk Decarboxylase from Bacillus Circulans Butirosin Biosynthesis

Popovic, B., Li, Y., Chirgadze, D.Y., Blundell, T.L., Spencer, J.B.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 48.18 kDa 
• Atom Count: 3,304 
• Modeled Residue Count: 391 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BTRK	A	428	Niallia circulans	Mutation(s): 0  EC: 4.1 (PDB Primary Data), 4.1.1.95 (UniProt)
UniProt
Find proteins for Q2L4H3 (Niallia circulans) Explore Q2L4H3  Go to UniProtKB:  Q2L4H3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.213 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.604	α = 90
b = 128.814	β = 90
c = 45.323	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-28 
Deposition Author(s): Popovic, B., Li, Y., Chirgadze, D.Y., Blundell, T.L., Spencer, J.B.

Revision History  

• Version 1.0: 2006-09-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description