Download MendeleyCrystal 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.
6X3M
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
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
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wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Hyaluronoglucosaminidase | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P15316 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
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, | 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 | 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 Name | Purpose |
|---|---|
| PHENIX | refinement |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2021-06-09 Deposition Author(s): Deivanayagam, C., Schormann, N.
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
