1H1A | pdb_00001h1a

Thermophilic beta-1,4-xylanase from Chaetomium thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.216 (Depositor) 
  • R-Value Work: 
    0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1H1A

This is version 2.2 of the entry. See complete history

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.Janis, J.Leisola, M.Rouvinen, J.

(2003) Eur J Biochem 270: 1399-1412

  • DOI: https://doi.org/10.1046/j.1432-1033.2003.03496.x
  • Primary Citation 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.


  • Organizational Affiliation
    • Department of Chemistry, University of Joensuu, Finland; Helsinki University of Technology, Finland. Nina.Hakulinen@joensuu.fi

Macromolecule Content 

  • Total Structure Weight: 42.51 kDa 
  • Atom Count: 3,637 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 382 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase
A, B
191Thermochaetoides thermophilaMutation(s): 0 
Gene Names: xyn11A
EC: 3.2.1.8
UniProt
Find proteins for Q8J1V6 (Thermochaetoides thermophila)
Explore Q8J1V6 
Go to UniProtKB:  Q8J1V6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8J1V6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNX

Query on UNX



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
UNKNOWN ATOM OR ION
X
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.216 (Depositor) 
  • R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.24α = 90
b = 57.15β = 90
c = 65.68γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-04
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2018-06-13
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2018-06-20
    Changes: Data collection, Structure summary
  • Version 2.0: 2020-03-11
    Changes: Derived calculations, Other, Polymer sequence
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary