4IXL | pdb_00004ixl

Crystal structure of endo-beta-1,4-xylanase from the alkaliphilic Bacillus sp. SN5

• PDB DOI: https://doi.org/10.2210/pdb4IXL/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-26 Released: 2014-02-12 
• Deposition Author(s): Bai, W.Q., Xue, Y.F., Huang, J.X., Zhou, C., Guo, R.T., Ma, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Structure Analysis of Alkaline xylanase from Alkaliphilic Bacillus sp. SN5 Implications for pH-dependent enzyme activity

Bai, W.Q., Xue, Y.F., Huang, J.X., Zhou, C., Guo, R.T., Ma, Y.H.

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)

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: 54.7 kDa 
• Atom Count: 4,324 
• Modeled Residue Count: 412 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
xylanase	A, B	244	Bacillus sp. (in: firmicutes)	Mutation(s): 0  Gene Names: Xyn11A-LC EC: 3.2.1.8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.415	α = 90
b = 59.415	β = 90
c = 153.736	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
APEX	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Bai, W.Q., Xue, Y.F., Huang, J.X., Zhou, C., Guo, R.T., Ma, Y.H.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description