6WV2

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

PDB DOI: https://doi.org/10.2210/pdb6WV2/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.213 (Depositor), 0.210 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 94.66 kDa
Atom Count: 6,383
Modelled Residue Count: 815
Deposited Residue Count: 879
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15316
Sequence Annotations Expand
Reference Sequence LOADING

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 D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.213 (Depositor), 0.210 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.451	α = 90
b = 86.789	β = 90
c = 168.152	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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

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.