1DBG

CRYSTAL STRUCTURE OF CHONDROITINASE B

• PDB DOI: https://doi.org/10.2210/pdb1DBG/pdb

• Classification: LYASE
• Organism(s): Pedobacter heparinus
• Mutation(s): No 


• Deposited: 1999-11-02 Released: 2000-01-12 
• Deposition Author(s): Huang, W., Matte, A., Li, Y., Kim, Y.S., Linhardt, R.J., Su, H., Cygler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.190 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.5 kDa 
• Atom Count: 4,364 
• Modelled Residue Count: 481 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHONDROITINASE B	A	506	Pedobacter heparinus	Mutation(s): 0
UniProt
Find proteins for Q46079 (Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3)) Explore Q46079  Go to UniProtKB:  Q46079

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-deoxy-alpha-D-glucopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose	B	7		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G76025BW GlyCosmos:  G76025BW

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.6	α = 90
b = 74.4	β = 92.9
c = 58.7	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-12 
Deposition Author(s): Huang, W., Matte, A., Li, Y., Kim, Y.S., Linhardt, R.J., Su, H., Cygler, M.

Revision History  

• Version 1.0: 2000-01-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary