3RO8

Crystal structure of the catalytic domain of XynA1 from Paenibacillus sp. JDR-2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1016/j.jsb.2012.09.007
  • Primary Citation of 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.

    • Organizational Affiliation: 

    Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA. fjstjohn@gmail.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase
A, B, C, D, E
A, B, C, D, E, F, G, H
341Paenibacillus sp. JDR-2Mutation(s): 0 
Gene Names: Pjdr2_0221
EC: 3.2.1.8
UniProt
Find proteins for C6CRV0 (Paenibacillus sp. (strain JDR-2))
Explore C6CRV0 
Go to UniProtKB:  C6CRV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6CRV0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
BA [auth H]
J [auth A]
M [auth B]
P [auth C]
R [auth D]
BA [auth H],
J [auth A],
M [auth B],
P [auth C],
R [auth D],
T [auth E],
U [auth E],
X [auth F],
Z [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
K [auth A]
L [auth B]
N [auth B]
AA [auth H],
I [auth A],
K [auth A],
L [auth B],
N [auth B],
O [auth C],
Q [auth D],
S [auth E],
V [auth E],
W [auth F],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.072α = 90
b = 93.172β = 99.96
c = 182.947γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2012-11-14
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations