2O92 | pdb_00002o92

Crystal structure of a signalling protein (SPG-40) complex with tetrasaccharide at 3.0A resolution

• PDB DOI: https://doi.org/10.2210/pdb2O92/pdb

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


• Deposited: 2006-12-13 Released: 2006-12-26 
• Deposition Author(s): Sharma, P., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a signalling protein (SPG-40) complex with tetrasaccharide at 3.0A resolution

Sharma, P., Singh, N., Sharma, S., Kaur, P., 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: 42.15 kDa 
• Atom Count: 3,005 
• Modeled 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	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-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G01361SX GlyCosmos:  G01361SX GlyGen:  G01361SX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.638	α = 90
b = 66.238	β = 90
c = 107.158	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Sharma, P., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2006-12-26
  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 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary