6R2J

Crystal Structure of Pseudomonas stutzeri endoglucanase Cel5A in complex with cellobiose

• PDB DOI: https://doi.org/10.2210/pdb6R2J/pdb

• Classification: HYDROLASE
• Organism(s): Stutzerimonas stutzeri A1501
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-18 Released: 2020-01-29 
• Deposition Author(s): Dutoit, R., Delsaute, M., Berlemont, R., Van Elder, D., Galleni, M., Bauvois, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.224 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Crystal structure determination of Pseudomonas stutzeri A1501 endoglucanase Cel5A: the search for a molecular basis for glycosynthesis in GH5_5 enzymes.

Dutoit, R., Delsaute, M., Collet, L., Vander Wauven, C., Van Elder, D., Berlemont, R., Richel, A., Galleni, M., Bauvois, C.

(2019) Acta Crystallogr D Struct Biol 75: 605-615

• DOI: https://doi.org/10.1107/S2059798319007113

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 150.04 kDa 
• Atom Count: 12,620 
• Modelled Residue Count: 1,310 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase(Endo-1,4-beta-glucanase)protein	A, B, C, D	330	Stutzerimonas stutzeri A1501	Mutation(s): 0  Gene Names: PST_2494
UniProt
Find proteins for A4VME5 (Stutzerimonas stutzeri (strain A1501)) Explore A4VME5  Go to UniProtKB:  A4VME5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	G [auth A], H [auth B], I [auth C], J [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	E, F	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.224 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.25	α = 90
b = 82.82	β = 91.97
c = 104.68	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Dutoit, R., Delsaute, M., Berlemont, R., Van Elder, D., Galleni, M., Bauvois, C.

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary