1H5V

Thiopentasaccharide complex of the endoglucanase Cel5A from Bacillus agaradharens at 1.1 A resolution in the tetragonal crystal form

• PDB DOI: https://doi.org/10.2210/pdb1H5V/pdb

• Classification: HYDROLASE
• Organism(s): Salipaludibacillus agaradhaerens
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2001-05-28 Released: 2002-05-23 
• Deposition Author(s): Varrot, A., Sulzenbacher, G., Schulein, M., Driguez, H., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 
• R-Value Observed: 0.121 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.49 kDa 
• Atom Count: 3,035 
• Modelled Residue Count: 301 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE 5A	A	304	Salipaludibacillus agaradhaerens	Mutation(s): 0  EC: 3.2.1.4
UniProt
Find proteins for O85465 (Salipaludibacillus agaradhaerens) Explore O85465  Go to UniProtKB:  O85465

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-alpha-D-glucopyranoside	B	5	N/A	N/A
Glycosylation Resources
GlyTouCan:  G68848DV GlyCosmos:  G68848DV

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 
• R-Value Observed: 0.121 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.169	α = 90
b = 75.169	β = 90
c = 135.471	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-23 
Deposition Author(s): Varrot, A., Sulzenbacher, G., Schulein, M., Driguez, H., Davies, G.J.

Revision History  

• Version 1.0: 2002-05-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-10-24
  Changes: Data collection, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary