1HIX | pdb_00001hix

CRYSTALLOGRAPHIC ANALYSES OF FAMILY 11 ENDO-BETA-1,4-XYLANASE XYL1 FROM STREPTOMYCES SP. S38

• PDB DOI: https://doi.org/10.2210/pdb1HIX/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. S38
• Expression System: Streptomyces lividans
• Mutation(s): No 


• Deposited: 2001-01-05 Released: 2001-11-30 
• Deposition Author(s): Wouters, J., Georis, J., Dusart, J., Frere, J.M., Depiereux, E., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.309 (Depositor) 
• R-Value Work: 
  0.211 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystallographic Analysis of Family 11 Endo-[Beta]-1,4-Xylanase Xyl1 from Streptomyces Sp. S38

Wouters, J., Georis, J., Engher, D., Vandenhaute, J., Dusart, J., Frere, J.M., Depiereux, E., Charlier, P.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1813

• PubMed: 11717493 
• DOI: https://doi.org/10.1107/s0907444901015153
• Primary Citation Related Structures: 
  1HIX


• PubMed Abstract: 
  

  Family 11 endo-beta-1,4-xylanases degrade xylan, the main constituent of plant hemicelluloses, and have many potential uses in biotechnology. The structure of Xyl1, a family 11 endo-xylanase from Streptomyces sp. S38, has been solved. The protein crystallized from ammonium sulfate in the trigonal space group P321, with unit-cell parameters a = b = 71.49, c = 130.30 A, gamma = 120.0 degrees. The structure was solved at 2.0 A by X-ray crystallography using the molecular-replacement method and refined to a final R factor of 18.5% (R(free) = 26.9%). Xyl1 has the overall fold characteristic of family 11 xylanases, with two highly twisted beta-sheets defining a long cleft containing the two catalytic residues Glu87 and Glu177.

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Organizational Affiliation: 
• Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre Dame de la Paix, 61 Rue de Bruxelles, B-5000 Namur, Belgium. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 41.19 kDa 
• Atom Count: 3,077 
• Modeled Residue Count: 372 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE	A, B	190	Streptomyces sp. S38	Mutation(s): 0  Gene Names: XYL1 EC: 3.2.1.8
UniProt
Find proteins for Q59962 (Streptomyces sp. S38) Explore Q59962  Go to UniProtKB:  Q59962

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.309 (Depositor) 
• R-Value Work:  0.211 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.493	α = 90
b = 71.493	β = 90
c = 130.298	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-30 
Deposition Author(s): Wouters, J., Georis, J., Dusart, J., Frere, J.M., Depiereux, E., Charlier, P.

Revision History  

• Version 1.0: 2001-11-30
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description