2YVV | pdb_00002yvv

Crystal structure of hyluranidase complexed with lactose at 2.6 A resolution reveals three specific sugar recognition sites

PDB DOI: https://doi.org/10.2210/pdb2YVV/pdb

Classification: LYASE
Organism(s): Streptococcus pyogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-16 Released: 2007-05-01
Deposition Author(s): Mishra, P., Prem Kumar, R., Singh, N., Sharma, S., Kaur, P., Perbandt, M., Betzel, C., Bhakuni, V., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.226 (Depositor)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of hyluranidase complexed with lactose at 2.6 A resolution reveals three specific sugar recognition sites

Mishra, P., Prem Kumar, R., Singh, N., Sharma, S., Kaur, P., Perbandt, M., Betzel, C., Bhakuni, V., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 37.5 kDa
Atom Count: 2,694
Modeled Residue Count: 332
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronidase, phage associated	A	338	Streptococcus pyogenes	Mutation(s): 0 Gene Names: HYL P2 EC: 4.2.2.1
UniProt
Find proteins for Q9A0M7 (Streptococcus pyogenes serotype M1) Explore Q9A0M7 Go to UniProtKB: Q9A0M7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9A0M7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	B, C, D	2		N/A	Interactions Focus chain B Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G88362QR GlyCosmos: G88362QR GlyGen: G88362QR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008 Query on PRD_900008	B, C, D	alpha-lactose	Oligosaccharide / Nutrient		Interactions Focus chain B Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.226 (Depositor)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.061	α = 90
b = 59.061	β = 90
c = 588.84	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary