Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.70 kDa 
• Atom Count: 1787 
• Modelled Residue Count: 197 
• Deposited Residue Count: 197 
• Unique protein chains: 1

1M4W

Thermophilic b-1,4-xylanase from Nonomuraea flexuosa

• PDB DOI: 10.2210/pdb1M4W/pdb

• Classification: HYDROLASE
• Organism(s): Thermopolyspora flexuosa
• Expression System: Trichoderma reesei
• Mutation(s): No 


• Deposited: 2002-07-05 Released: 2003-07-08 
• Deposition Author(s): Hakulinen, N., Turunen, O., Janis, J., Leisola, M., Rouvinen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.209 
• R-Value Work: 0.146 

Literature

Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability.

Hakulinen, N., Turunen, O., Leisola, M., Rouvinen, J.

(2003) Eur J Biochem 270: 1399-1412

• PubMed: 12653995 
• DOI: 10.1046/j.1432-1033.2003.03496.x
• Primary Citation of Related Structures:  
  1H1A, 1M4W


• PubMed Abstract: 
  

The crystal structures of thermophilic xylanases from Chaetomium thermophilum and Nonomuraea flexuosa were determined at 1.75 and 2.1 A resolution, respectively. Both enzymes have the overall fold typical to family 11 xylanases with two highly twisted beta-sheets forming a large cleft. The comparison of 12 crystal structures of family 11 xylanases from both mesophilic and thermophilic organisms showed that the structures of different xylanases are very similar. The sequence identity differences correlated well with the structural differences. Several minor modifications appeared to be responsible for the increased thermal stability of family 11 xylanases: (a) higher Thr : Ser ratio (b) increased number of charged residues, especially Arg, resulting in enhanced polar interactions, and (c) improved stabilization of secondary structures involved the higher number of residues in the beta-strands and stabilization of the alpha-helix region. Some members of family 11 xylanases have a unique strategy to improve their stability, such as a higher number of ion pairs or aromatic residues on protein surface, a more compact structure, a tighter packing, and insertions at some regions resulting in enhanced interactions.

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Organizational Affiliation: 

Department of Chemistry, University of Joensuu, Finland; Helsinki University of Technology, Finland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endoxylanase	A	197	Thermopolyspora flexuosa	Mutation(s): 0  Gene Names: xyn11A, FHX40_0105 EC: 3.2.1.8
UniProt
Find proteins for Q8GMV7 (Thermopolyspora flexuosa) Explore Q8GMV7  Go to UniProtKB:  Q8GMV7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.209 
• R-Value Work: 0.146 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.034	α = 90
b = 37.034	β = 90
c = 191.808	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-05 
• Released Date: 2003-07-08 
Deposition Author(s): Hakulinen, N., Turunen, O., Janis, J., Leisola, M., Rouvinen, J.

Revision History  

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary