5WH8

Cellulase Cel5C_n

• PDB DOI: https://doi.org/10.2210/pdb5WH8/pdb

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


• Deposited: 2017-07-15 Released: 2018-03-14 
• Deposition Author(s): Koropatkin, N.M., Pope, P.B., Naas, A.E.
• Funding Organization(s): Research Council of Norway, European Research Commission Starting Grant Fellowship

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.174 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 

Literature

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.

Naas, A.E., Solden, L.M., Norbeck, A.D., Brewer, H., Hagen, L.H., Heggenes, I.M., McHardy, A.C., Mackie, R.I., Pasa-Tolic, L., Arntzen, M.O., Eijsink, V.G.H., Koropatkin, N.M., Hess, M., Wrighton, K.C., Pope, P.B.

(2018) Microbiome 6: 44-44

• PubMed: 29490697 
• DOI: https://doi.org/10.1186/s40168-018-0421-8
• Primary Citation of Related Structures:  
  5WH8


• PubMed Abstract: 
  

  In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa.

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Organizational Affiliation: 

Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway.

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: 38.11 kDa 
• Atom Count: 2,920 
• Modelled Residue Count: 323 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative carbohydrate-active enzyme	A	323	uncultured organism	Mutation(s): 0  Gene Names: SARM_0026
UniProt
Find proteins for E9NSK2 (uncultured organism) Explore E9NSK2  Go to UniProtKB:  E9NSK2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	O [auth A], P [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
MES	Q [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.174 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.21	α = 90
b = 75.5	β = 90
c = 88.83	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Koropatkin, N.M., Pope, P.B., Naas, A.E.

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	214042
European Research Commission Starting Grant Fellowship	Norway	336355 - MicroDE

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description