6WXA | pdb_00006wxa

Crystal structure of truncated Streptococcal bacteriophage hyaluronidase complexed with unsaturated hyaluronan hexa-saccharides

• PDB DOI: https://doi.org/10.2210/pdb6WXA/pdb

• Classification: LYASE
• Organism(s): Streptococcus pyogenes phage H4489A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-10 Released: 2021-05-12 
• Deposition Author(s): Deivanayagam, C., Schormann, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.213 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic Collagen and Elucidation of Catalytic Mechanism

Lee, J.H., Schormann, N., Rajashankar, K.R., Deivanaygam, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 99.43 kDa 
• Atom Count: 6,656 
• Modeled Residue Count: 825 
• Deposited Residue Count: 879 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronan lyase	A, B, C	293	Streptococcus pyogenes phage H4489A	Mutation(s): 0  Gene Names: HYLP1, HYLP EC: 4.2.2.1 (PDB Primary Data), 3.2.1.35 (UniProt)
UniProt
Find proteins for P15316 (Streptococcus pyogenes phage H4489A) Explore P15316  Go to UniProtKB:  P15316

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	6		N/A
Glycosylation Resources
GlyTouCan: G36225QF GlyCosmos: G36225QF

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	5		N/A
Glycosylation Resources
GlyTouCan: G35556TW GlyCosmos: G35556TW GlyGen: G35556TW

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H	4		N/A
Glycosylation Resources
GlyTouCan: G58744KX GlyCosmos: G58744KX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI (Subject of Investigation/LOI)	I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.213 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.296	α = 90
b = 86.492	β = 90
c = 168.226	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Deivanayagam, C., Schormann, N.

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description