4XAD | pdb_00004xad

Crystal structure of hen egg white lysozyme in complex with Galf-GlcNAc

• PDB DOI: https://doi.org/10.2210/pdb4XAD/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2014-12-14 Released: 2014-12-31 
• Deposition Author(s): Wangkanont, K., Kiessling, L.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.168 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of hen egg white lysozyme in complex with Galf-GlcNAc, an O-linked disaccharide core from Trypanosoma cruzi

Wangkanont, K., Kiessling, L.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 14.93 kDa 
• Atom Count: 1,326 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactofuranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G68826FE GlyCosmos: G68826FE GlyGen: G68826FE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.168 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.002	α = 90
b = 78.002	β = 90
c = 37.709	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Wangkanont, K., Kiessling, L.L.

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary