6SNU

Crystal structure of the W60C mutant of the (S)-selective transaminase from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb6SNU/pdb

• Classification: TRANSFERASE
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-08-27 Released: 2019-10-09 
• Deposition Author(s): Ruggieri, F., Gustafsson, C., Kimbung, R.Y., Walse, B., Logan, D.T., Berglund, P.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Crystal Structures Combined with Molecular Dynamics Reveal Altered Flow of Water in the Active Site of W60C Chromobacterium violaceum omega-transaminase

Ruggieri, F., Gustafsson, C., Kimbung, R.Y., Walse, B., Logan, D.T., Berglund, P.

Not 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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 209.53 kDa 
• Atom Count: 14,564 
• Modelled Residue Count: 1,814 
• Deposited Residue Count: 1,860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase family protein	A, B, C, D	465	Chromobacterium violaceum	Mutation(s): 1  Gene Names: bioK, CBW21_20070, NCTC8684_01926 EC: 2.6.1
UniProt
Find proteins for A0A1R0MXM9 (Chromobacterium violaceum) Explore A0A1R0MXM9  Go to UniProtKB:  A0A1R0MXM9

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.221	α = 75.03
b = 62.196	β = 81.31
c = 118.423	γ = 75.3

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Ruggieri, F., Gustafsson, C., Kimbung, R.Y., Walse, B., Logan, D.T., Berglund, P.

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Funding Organization	Location	Grant Number
European Union	Sweden	634200

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description