2DRJ | pdb_00002drj

Xray structure of alpha-2,3/8-sialyltransferase CstII F91Y mutant

• PDB DOI: https://doi.org/10.2210/pdb2DRJ/pdb

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


• Deposited: 2006-06-09 Released: 2007-04-24 
• Deposition Author(s): Chiu, C.P.C., Strynadka, N.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.261 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

High-throughput screening methodology for the directed evolution of glycosyltransferases

Aharoni, A., Thieme, K., Chiu, C.P.C., Buchini, S., Lairson, L.L., Chen, H., Strynadka, N.C.J., Wakarchuk, W.W., Withers, S.G.

(2006) Nat Methods 3: 609-614

• PubMed: 16862130 
• DOI: https://doi.org/10.1038/nmeth0806-589
• Primary Citation Related Structures: 
  2DRJ

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.57 kDa 
• Atom Count: 2,091 
• Modeled Residue Count: 233 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-2,3/8-sialyltransferase	A	262	Campylobacter jejuni	Mutation(s): 3  EC: 2.4.99
UniProt
Find proteins for Q9LAK3 (Campylobacter jejuni) Explore Q9LAK3  Go to UniProtKB:  Q9LAK3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CSF	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID C20 H30 F N4 O16 P HNJLGUNKGJTPBF-JTKQZVQZSA-N
IPA	C [auth A], D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.261 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.653	α = 90
b = 116.653	β = 90
c = 44.086	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Chiu, C.P.C., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.6: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary