2YVV | pdb_00002yvv

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

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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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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hyaluronidase, phage associated338Streptococcus pyogenesMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A0M7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
B, C, D
2N/A
Glycosylation Resources
GlyTouCan:  G88362QR
GlyCosmos:  G88362QR
GlyGen:  G88362QR
Biologically Interesting Molecules (External Reference) 1 Unique
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 = 59.061α = 90
b = 59.061β = 90
c = 588.84γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

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