5E9P | pdb_00005e9p

Spirochaeta thermophila X module - CBM64 - wildtype

• PDB DOI: https://doi.org/10.2210/pdb5E9P/pdb

• Classification: HYDROLASE
• Organism(s): Winmispira thermophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-15 Released: 2016-03-02 
• Deposition Author(s): Schiefner, A., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.125 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.106 (Depositor) 
• R-Value Observed: 
  0.107 (Depositor) 

Starting Model: experimental

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

• PubMed: 26868291 
• DOI: https://doi.org/10.1002/prot.25010
• Primary Citation 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.

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

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 10.13 kDa 
• Atom Count: 932 
• Modeled Residue Count: 86 
• Deposited Residue Count: 86 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulase, glycosyl hydrolase family 5, TPS linker, domain X	A	86	Winmispira thermophila	Mutation(s): 0  Gene Names: STHERM_c20620 EC: 3.2.1.4
UniProt
Find proteins for E0RQU0 (Winmispira thermophila (strain ATCC 49972 / DSM 6192 / RI 19.B1)) Explore E0RQU0  Go to UniProtKB:  E0RQU0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.125 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.106 (Depositor) 
• R-Value Observed: 0.107 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.517	α = 90
b = 58.517	β = 90
c = 33.437	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Schiefner, A., Skerra, A.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description