7L74 | pdb_00007l74

Crystal structure of Beta-hexosyl transferase from Hamamotoa (Sporobolomyces) singularis bound to TRIS

• PDB DOI: https://doi.org/10.2210/pdb7L74/pdb

• Classification: TRANSFERASE
• Organism(s): Hamamotoa singularis
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2020-12-25 Released: 2022-02-09 
• Deposition Author(s): Dagher, S.F., Edwards, B.F.P., Meilleur, F., Bruno-Barcena, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: in silico

Literature

Structure and mutagenic analysis of the Beta-hexosyltransferase from Hamamotoa (Sporobolomyces) singularis

Dagher, S.F., Edwards, B.F.P., Meilleur, F., Bruno-Barcena, J.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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 132.85 kDa 
• Atom Count: 9,347 
• Modeled Residue Count: 1,083 
• Deposited Residue Count: 1,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hexosyltransferase	A, B	578	Hamamotoa singularis	Mutation(s): 0  Gene Names: bglA
UniProt
Find proteins for Q564N5 (Hamamotoa singularis) Explore Q564N5  Go to UniProtKB:  Q564N5
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G, H, I, J	2	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS (Subject of Investigation/LOI)	L [auth A], M [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CA (Subject of Investigation/LOI)	K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.319	α = 90
b = 63.209	β = 100.42
c = 105.006	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Dagher, S.F., Edwards, B.F.P., Meilleur, F., Bruno-Barcena, J.M.

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary