2B31

Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 3.1 A resolution reveals large scale conformational changes in the residues of TIM barrel

• PDB DOI: https://doi.org/10.2210/pdb2B31/pdb
• Entry: 2B31 supersedes: 1ZU9

• Classification: SIGNALING PROTEIN
• Organism(s): Capra hircus
• Mutation(s): No 


• Deposited: 2005-09-19 Released: 2005-09-27 
• Deposition Author(s): Ethayathulla, A.S., Kumar, J., Srivastava, D.B., Singh, N., Sharma, S., Bhushan, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.218 (Depositor) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 3.1 A resolution reveals large scale conformational changes in the residues of TIM barrel

Ethayathulla, A.S., Kumar, J., Srivastava, D.B., Singh, N., Sharma, S., Bhushan, A., Singh, T.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.19 kDa 
• Atom Count: 3,045 
• Modelled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-3-like protein 1, SPG-40	A	361	Capra hircus	Mutation(s): 0
UniProt
Find proteins for Q8SPQ0 (Capra hircus) Explore Q8SPQ0  Go to UniProtKB:  Q8SPQ0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G10234TF GlyCosmos:  G10234TF GlyGen:  G10234TF

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.218 (Depositor) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.745	α = 90
b = 66.613	β = 90
c = 107.812	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Ethayathulla, A.S., Kumar, J., Srivastava, D.B., Singh, N., Sharma, S., Bhushan, A., Singh, T.P.
• This entry supersedes: 1ZU9

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary