1NQ6 | pdb_00001nq6

Crystal Structure of the catalytic domain of xylanase A from Streptomyces halstedii JM8

• PDB DOI: https://doi.org/10.2210/pdb1NQ6/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces halstedii
• Expression System: Streptomyces parvulus
• Mutation(s): No 


• Deposited: 2003-01-21 Released: 2004-01-21 
• Deposition Author(s): Canals, A., Vega, M.C., Gomis-Ruth, F.X., Santamaria, R.I., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.176 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Structure of xylanase Xys1delta from Streptomyces halstedii.

Canals, A., Vega, M.C., Gomis-Ruth, F.X., Diaz, M., Santamaria R, R.I., Coll, M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1447-1453

• PubMed: 12876348 
• DOI: https://doi.org/10.1107/s0907444903012629
• Primary Citation Related Structures: 
  1NQ6


• PubMed Abstract: 
  

  Xylanases hydrolyze the beta-1,4-linked xylose backbone of xylans. They are of increasing interest in the paper and food industries for their pre-bleaching and bio-pulping applications. Such industries demand new xylanases to cover a wider range of cleavage specificity, activity and stability. The catalytic domain of xylanase Xys1 from Streptomyces halstedii JM8 was expressed, purified and crystallized and native data were collected to 1.78 A resolution with an R(merge) of 4.4%. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 34.05, b = 79.60, c = 87.80 A. The structure was solved by the molecular-replacement method using the structure of the homologue Xyl10A from Streptomyces lividans. In a similar manner to other members of its family, Xys1 folds to form a standard (beta/alpha)(8) barrel with the two catalytic functions, the acid/base and the nucleophile, at its C-terminal side. The overall structure is described and compared with those of related xylanases.

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Organizational Affiliation: 
• Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona 18-26, 08034 Barcelona, Spain. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.64 kDa 
• Atom Count: 2,642 
• Modeled Residue Count: 302 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xys1	A	302	Streptomyces halstedii	Mutation(s): 0  Gene Names: xysA EC: 3.2.1.8
UniProt
Find proteins for Q59922 (Streptomyces halstedii) Explore Q59922  Go to UniProtKB:  Q59922

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.176 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.05	α = 90
b = 79.6	β = 90
c = 87.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-21 
Deposition Author(s): Canals, A., Vega, M.C., Gomis-Ruth, F.X., Santamaria, R.I., Coll, M.

Revision History  

• Version 1.0: 2004-01-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary