7W1D

Crystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide lyase in a C2 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


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Literature

Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use.

Tu, I.F.Lin, T.L.Yang, F.L.Lee, I.M.Tu, W.L.Liao, J.H.Ko, T.P.Wu, W.J.Jan, J.T.Ho, M.R.Chou, C.Y.Wang, A.H.Wu, C.Y.Wang, J.T.Huang, K.F.Wu, S.H.

(2022) J Biomed Sci 29: 9-9

  • DOI: https://doi.org/10.1186/s12929-022-00792-4
  • Primary Citation of Related Structures:  
    7W1C, 7W1D, 7W1E

  • PubMed Abstract: 

    K1 capsular polysaccharide (CPS)-associated Klebsiella pneumoniae is the primary cause of pyogenic liver abscesses (PLA) in Asia. Patients with PLA often have serious complications, ultimately leading to a mortality of ~ 5%. This K1 CPS has been reported as a promising target for development of glycoconjugate vaccines against K. pneumoniae infection. The pyruvylation and O-acetylation modifications on the K1 CPS are essential to the immune response induced by the CPS. To date, however, obtaining the fragments of K1 CPS that contain the pyruvylation and O-acetylation for generating glycoconjugate vaccines still remains a challenge.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
K1 LYASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
671Klebsiella phage NTUH-K2044-K1-1Mutation(s): 2 
UniProt
Find proteins for A0A068Q5Q5 (Klebsiella phage NTUH-K2044-K1-1)
Explore A0A068Q5Q5 
Go to UniProtKB:  A0A068Q5Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068Q5Q5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT (Subject of Investigation/LOI)
Query on CIT

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth K]
DA [auth K]
EA [auth L]
M [auth A]
AA [auth J],
BA [auth K],
DA [auth K],
EA [auth L],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
S [auth D],
T [auth E],
U [auth F],
V [auth F],
W [auth G],
Y [auth H],
Z [auth I]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
CO3 (Subject of Investigation/LOI)
Query on CO3

Download Ideal Coordinates CCD File 
CA [auth K],
R [auth C],
X [auth H]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 363.945α = 90
b = 239.626β = 100.13
c = 121.632γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST-108-2113-M-001-008
Academia Sinica (Taiwan)TaiwanAS-KPQ-110-ITAR-11

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release