4M24 | pdb_00004m24

Crystal structure of the endo-1,4-glucanase, RBcel1, in complex with cellobiose

• PDB DOI: https://doi.org/10.2210/pdb4M24/pdb

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


• Deposited: 2013-08-05 Released: 2014-12-31 
• Deposition Author(s): Delsaute, M., Berlemont, R., Van elder, D., Galleni, M., Bauvois, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.149 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.124 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Characterisation of two GH family 5 cellulases required for bacterial cellulose production

Delsaute, M., Bauvois, C., Wei, Q., Dehareng, D., Byttebier, V., Van elder, D., Paquot, M., Cornelis, P., Galleni, M., Berlemont, R.

To be published.

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: 36.97 kDa 
• Atom Count: 3,310 
• Modeled Residue Count: 321 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A	321	uncultured bacterium	Mutation(s): 0  EC: 3.2.1.4
UniProt
Find proteins for A0ACD6B8G5 (uncultured bacterium) Explore A0ACD6B8G5  Go to UniProtKB:  A0ACD6B8G5

Oligosaccharides

Help  

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A], D [auth A]	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	B	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.149 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.124 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.7	α = 90
b = 63.25	β = 90
c = 98.53	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Delsaute, M., Berlemont, R., Van elder, D., Galleni, M., Bauvois, C.

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary