6WWX | pdb_00006wwx

Crystal structure of truncated bacteriophage hyaluronan lyase HylP in complex with unsaturated hyaluronan tetra-saccharides

PDB DOI: https://doi.org/10.2210/pdb6WWX/pdb

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

Deposited: 2020-05-09 Released: 2021-05-12
Deposition Author(s): Deivanayagam, C., Schormann, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.210 (Depositor), 0.214 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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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.

Macromolecule Content

Total Structure Weight: 99.21 kDa
Atom Count: 6,771
Modeled Residue Count: 816
Deposited Residue Count: 879
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronoglucosaminidase	A, B, C	293	Streptococcus pyogenes phage H4489A	Mutation(s): 0 Gene Names: HYLP1, HYLP EC: 3.2.1.35
UniProt
Find proteins for P15316 (Streptococcus pyogenes phage H4489A) Explore P15316 Go to UniProtKB: P15316
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15316
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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	D, E, F, G, H D, E, F, G, H, I	4		N/A	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G58744KX GlyCosmos: G58744KX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.210 (Depositor), 0.214 (DCC)
R-Value Work: 0.182 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.535	α = 90
b = 86.819	β = 90
c = 168.646	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Deivanayagam, C.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.