5E9O | pdb_00005e9o

Spirochaeta thermophila X module - CBM64 - mutant G504A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for cellulose binding by the type A carbohydrate-binding module 64 of Spirochaeta thermophila.

Schiefner, A.Angelov, A.Liebl, W.Skerra, A.

(2016) Proteins 84: 855-858

  • DOI: https://doi.org/10.1002/prot.25010
  • Primary Citation of Related Structures:  
    5E9O, 5E9P

  • PubMed Abstract: 

    Spirochaeta thermophila secretes seven glycoside hydrolases for plant biomass degradation that carry a carbohydrate-binding module 64 (CBM64) appended at the C-terminus. CBM64 adsorbs to various β1-4-linked pyranose substrates and shows high affinity for cellulose. We present the first crystal structure of a CBM64 at 1.2 Å resolution, which reveals a jelly-roll-like fold corresponding to a surface-binding type A CBM. Modeling of its interaction with cellulose indicates that CBM64 achieves association with the hydrophobic face of β-linked pyranose chains via a unique coplanar arrangement of four exposed tryptophan side chains. Proteins 2016; 84:855-858. © 2016 Wiley Periodicals, Inc.


  • Organizational Affiliation
    • Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising (Weihenstephan), Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
A, B, C, D
86Winmispira thermophilaMutation(s): 1 
Gene Names: STHERM_c20620
EC: 3.2.1.4
UniProt
Find proteins for E0RQU0 (Spirochaeta thermophila (strain ATCC 49972 / DSM 6192 / RI 19.B1))
Explore E0RQU0 
Go to UniProtKB:  E0RQU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0RQU0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.929α = 90
b = 144.929β = 90
c = 144.929γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Derived calculations
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references