3JU4 | pdb_00003ju4

Crystal Structure Analysis of EndosialidaseNF at 0.98 A Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 
    0.133 (Depositor), 0.134 (DCC) 
  • R-Value Work: 
    0.116 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 
    0.116 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure analysis of endosialidase NF at 0.98 A resolution.

Schulz, E.C., Neumann, P., Gerardy-Schahn, R., Sheldrick, G.M., Ficner, R.

(2010) Acta Crystallogr D Biol Crystallogr 66: 176-180

  • DOI: https://doi.org/10.1107/S0907444909048720
  • Primary Citation Related Structures: 
    3JU4

  • PubMed Abstract: 

    Endosialidase NF (endoNF) is a bacteriophage-derived endosialidase that specifically degrades alpha-2,8-linked polysialic acid. The structure of a new crystal form of endoNF in complex with sialic acid has been refined at 0.98 A resolution. The 210 kDa homotrimeric multi-domain enzyme displays outstanding stability and resistance to SDS. Even at atomic resolution, only a minor fraction of side chains possess alternative conformations. However, multiple conformations of an active-site residue imply that it has an important catalytic function in the cleavage mechanism of polysialic acid.

    • Organizational Affiliation: 
    • Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 75.05 kDa 
  • Atom Count: 7,145 
  • Modeled Residue Count: 670 
  • Deposited Residue Count: 670 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endo-N-acetylneuraminidase670Escherichia phage K1FMutation(s): 0 
EC: 3.2.1.129
UniProt
Find proteins for Q04830 (Escherichia phage K1F)
Explore Q04830 
Go to UniProtKB:  Q04830
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04830
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SLB

Query on SLB


Download:Ideal Coordinates CCD File
B [auth A]N-acetyl-beta-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-PFQGKNLYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA


Download:Ideal Coordinates CCD File
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free:  0.133 (Depositor), 0.134 (DCC) 
  • R-Value Work:  0.116 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 0.116 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.04α = 90
b = 119.04β = 90
c = 175.69γ = 120
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary