4R4X

Structure of PNGF-II in C2 space group

• PDB DOI: https://doi.org/10.2210/pdb4R4X/pdb

• Classification: HYDROLASE
• Organism(s): Elizabethkingia meningoseptica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-20 Released: 2015-01-28 
• Deposition Author(s): Sun, G., Yu, X., Celimuge, Wang, L., Li, M., Gan, J., Qu, D., Ma, J., Chen, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Literature

Identification and Characterization of a Novel Prokaryotic Peptide: N-glycosidase from Elizabethkingia meningoseptica

Sun, G., Yu, X., Celimuge, Wang, L., Li, M., Gan, J., Qu, D., Ma, J., Chen, L.

(2015) J Biol Chem 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61.66 kDa 
• Atom Count: 4,780 
• Modelled Residue Count: 544 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PNGF-II	A	546	Elizabethkingia meningoseptica	Mutation(s): 0  Gene Names: CP006576 EC: 2.7.7.7
UniProt
Find proteins for A0A090KI56 (Elizabethkingia meningoseptica) Explore A0A090KI56  Go to UniProtKB:  A0A090KI56

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.4	α = 90
b = 55.4	β = 102.2
c = 71.2	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Sun, G., Yu, X., Celimuge, Wang, L., Li, M., Gan, J., Qu, D., Ma, J., Chen, L.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection