8VR3

crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of its internal aldimine

• PDB DOI: https://doi.org/10.2210/pdb8VR3/pdb

• Classification: TRANSFERASE
• Organism(s): Psychrobacter cryohalolentis K5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-20 Released: 2024-01-31 
• Deposition Author(s): Bockhaus, N.J., Thoden, J.B., Holden, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5

Bockhaus, N.J., Dunsirn, M.M., Thoden, J.B., Holden, H.M.

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 PISA (software)

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: 83.68 kDa 
• Atom Count: 6,392 
• Modelled Residue Count: 744 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegT/DnrJ/EryC1/StrS aminotransferase	A, B	374	Psychrobacter cryohalolentis K5	Mutation(s): 0  Gene Names: Pcryo_0618
UniProt
Find proteins for Q1QD52 (Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5)) Explore Q1QD52  Go to UniProtKB:  Q1QD52

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ADI	F [auth B], G [auth B]	2,2'-(1,4-diazepane-1,4-diyl)di(ethane-1-sulfonic acid) C9 H20 N2 O6 S2 QZTMPPUJIVQNKS-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.019	α = 90
b = 157.97	β = 90
c = 130.591	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Bockhaus, N.J., Thoden, J.B., Holden, H.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM134643

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release