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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.58 Å
R-Value Free:
0.299 (Depositor), 0.301 (DCC)
R-Value Work:
0.247 (Depositor), 0.249 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Models: experimental
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This is version 1.1 of the entry. See complete history.

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

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronoglucosaminidase	A, B, C, D, E 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
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	AA [auth a], J, N, O, Q, AA [auth a], J, N, O, Q, T, U, V, Z	4		N/A	Interactions Focus chain AA [auth a] Focus chain J Focus chain N Focus chain O Focus chain Q Focus chain T Focus chain U Focus chain V Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain J Focus chain N Focus chain O Focus chain Q Focus chain T Focus chain U Focus chain V Focus chain Z
Glycosylation Resources
GlyTouCan: G58744KX GlyCosmos: G58744KX

Entity ID: 3
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-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L, M, P, R K, L, M, P, R, S, W, X, Y	8		N/A	Interactions Focus chain K Focus chain L Focus chain M Focus chain P Focus chain R Focus chain S Focus chain W Focus chain X Focus chain Y Interactions & Density Focus chain K Focus chain L Focus chain M Focus chain P Focus chain R Focus chain S Focus chain W Focus chain X Focus chain Y
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), 0.301 (DCC)
R-Value Work: 0.247 (Depositor), 0.249 (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

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Entry History

Deposition Data

Released Date: 2021-06-09

Deposition Author(s):

Deivanayagam, C.

Revision History (Full details and data files)

Version 1.0: 2021-06-09
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.