6X3M | pdb_00006x3m

Crystal structure of full-length Streptococcal bacteriophage hyaluronidase in complex with unsaturated hyaluronan octa-saccharides

• PDB DOI: https://doi.org/10.2210/pdb6X3M/pdb

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


• Deposited: 2020-05-21 Released: 2021-06-09 
• Deposition Author(s): Deivanayagam, C., Schormann, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free: 
  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Models: 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: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 386.29 kDa 
• Atom Count: 25,574 
• Modeled Residue Count: 3,241 
• Deposited Residue Count: 3,411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronoglucosaminidase	A, B, C, D, E, F, G, H, I	379	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	3D 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	AA [auth a], J, N, O, Q, T, U, V, Z	4		N/A
Glycosylation Resources
GlyTouCan:  G58744KX GlyCosmos:  G58744KX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L, M, P, R, S, W, X, Y	8		N/A
Glycosylation Resources
GlyTouCan:  G31971KV GlyCosmos:  G31971KV

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 338.168	α = 90
b = 56.797	β = 126.68
c = 276.954	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Deivanayagam, C., Schormann, N.

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description