4E4P | pdb_00004e4p

Second native structure of Xylanase A1 from Paenibacillus sp. JDR-2

• PDB DOI: https://doi.org/10.2210/pdb4E4P/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus sp. JDR-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-13 Released: 2012-04-18 
• Deposition Author(s): Pozharski, E., St John, F.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.295 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Literature

Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2.

St John, F.J., Preston, J.F., Pozharski, E.

(2012) J Struct Biol 180: 303-311

• PubMed: 23000703 
• DOI: https://doi.org/10.1016/j.jsb.2012.09.007
• Primary Citation Related Structures: 
  3RDK, 3RO8, 4E4P


• PubMed Abstract: 
  

  The Gram-positive bacterium Paenibacillus sp. JDR-2 (PbJDR2) has been shown to have novel properties in the utilization of the abundant but chemically complex hemicellulosic sugar glucuronoxylan. Xylanase A1 of PbJDR2 (PbXynA1) has been implicated in an efficient process in which extracellular depolymerization of this polysaccharide is coupled to assimilation and intracellular metabolism. PbXynA1is a 154kDa cell wall anchored multimodular glycosyl hydrolase family 10 (GH10) xylanase. In this work, the 38kDa catalytic module of PbXynA1 has been structurally characterized revealing several new features not previously observed in structures of GH10 xylanases. These features are thought to facilitate hydrolysis of highly substituted, chemically complex xylans that may be the form found in close proximity to the cell wall of PbJDR2, an organism shown to have a preference for growth on polymeric glucuronoxylan.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.97 kDa 
• Atom Count: 4,878 
• Modeled Residue Count: 586 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase A	A, B	341	Paenibacillus sp. JDR-2	Mutation(s): 0  Gene Names: Pjdr2_0221, xynA, xynA1 EC: 3.2.1.8
UniProt
Find proteins for C6CRV0 (Paenibacillus sp. (strain JDR-2)) Explore C6CRV0  Go to UniProtKB:  C6CRV0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.295 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.518	α = 90
b = 58.528	β = 108.81
c = 65.024	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Pozharski, E., St John, F.J.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references
• Version 1.2: 2012-11-14
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations