4Y9V | pdb_00004y9v

Gp54 tailspike of Acinetobacter baumannii bacteriophage AP22 in complex with A. baumannii capsular saccharide

• PDB DOI: https://doi.org/10.2210/pdb4Y9V/pdb

• Classification: LYASE
• Organism(s): Acinetobacter phage AP22
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2015-02-17 Released: 2017-02-01 
• Deposition Author(s): Buth, S.A., Shneider, M.M., Leiman, P.G.
• Funding Organization(s): Ecole Polytechnique Federale de Lausanne

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 
  0.109 (Depositor), 0.111 (DCC) 
• R-Value Work: 
  0.097 (Depositor), 0.107 (DCC) 
• R-Value Observed: 
  0.097 (Depositor) 

Literature

Structure of Acinetobacter baumannii bacteriophage AP22 polysaccharide degrading lyase in complex with A. baumannii capsular saccharide at 0.9 A resolution

Buth, S.A., Shneider, M.M., Leiman, P.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.1 kDa 
• Atom Count: 6,900 
• Modeled Residue Count: 603 
• Deposited Residue Count: 625 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Particle-associated lyase	A	625	Acinetobacter phage AP22	Mutation(s): 0
UniProt
Find proteins for I2GUG1 (Acinetobacter phage AP22) Explore I2GUG1  Go to UniProtKB:  I2GUG1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2,4-dideoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-alpha-D-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-mannopyranuronic acid	B	3		N/A
Glycosylation Resources
GlyTouCan: G54331LR GlyCosmos: G54331LR

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	M [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free:  0.109 (Depositor), 0.111 (DCC) 
• R-Value Work:  0.097 (Depositor), 0.107 (DCC) 
• R-Value Observed: 0.097 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.634	α = 90
b = 92.634	β = 90
c = 391.478	γ = 120

Software Package:

Software Name	Purpose
Coot	model building
XDS	data reduction
XSCALE	data scaling
SHELX	phasing
SHELXL	refinement
SHELXL-97	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Buth, S.A., Shneider, M.M., Leiman, P.G.

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Funding Organization	Location	Grant Number
Ecole Polytechnique Federale de Lausanne	Switzerland	0577-1

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-02-15
  Changes: Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Structure summary