2DRJ

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.261
R-Value Work: 0.194
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/nmeth0806-589
Primary Citation of Related Structures:
2DRJ

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9LAK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CSF Query on CSF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID C₂₀ H₃₀ F N₄ O₁₆ P HNJLGUNKGJTPBF-JTKQZVQZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A]	C [auth A], D [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.261
R-Value Work: 0.194
R-Value Observed: 0.197
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-04-24

Deposition Author(s):

Strynadka, N.C.J.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.