1OD3

Structure of CSCBM6-3 From Clostridium stercorarium in complex with laminaribiose

• PDB DOI: https://doi.org/10.2210/pdb1OD3/pdb

• Classification: HYDROLASE
• Organism(s): Thermoclostridium stercorarium
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-02-12 Released: 2003-03-13 
• Deposition Author(s): Boraston, A.B., Notenboom, V., Warren, R.A.J., Kilburn, D.G., Rose, D.R., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.149 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 

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: 18.19 kDa 
• Atom Count: 1,337 
• Modelled Residue Count: 132 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE XYLANASE	A	168	Thermoclostridium stercorarium	Mutation(s): 0
UniProt
Find proteins for Q8GJ44 (Thermoclostridium stercorarium) Explore Q8GJ44  Go to UniProtKB:  Q8GJ44

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan:  G36535HU GlyCosmos:  G36535HU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024	B, C	beta-laminaribiose	Oligosaccharide / Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.149 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.183	α = 90
b = 52.154	β = 90
c = 64.755	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-13 
Deposition Author(s): Boraston, A.B., Notenboom, V., Warren, R.A.J., Kilburn, D.G., Rose, D.R., Davies, G.J.

Revision History  

• Version 1.0: 2003-03-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary