4R4Z | pdb_00004r4z

Structure of PNGF-II in P21 space group

• PDB DOI: https://doi.org/10.2210/pdb4R4Z/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: 2.81 Å
• R-Value Free: 
  0.257 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

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 Biological Chem 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 244.12 kDa 
• Atom Count: 17,034 
• Modeled Residue Count: 2,154 
• Deposited Residue Count: 2,176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PNGF-II	A, B, C, D	544	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.257 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.8	α = 90
b = 94.2	β = 91.4
c = 165.8	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, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary