1XRV | pdb_00001xrv

Crystal Structure of the novel secretory signalling protein from Porcine (SPP-40) at 2.1A resolution.

• PDB DOI: https://doi.org/10.2210/pdb1XRV/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2004-10-16 Released: 2004-11-02 
• Deposition Author(s): Srivastava, D.B., Ethayathulla, A.S., Singh, N., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the novel secretory signalling protein from Porcine (SPP-40) at 2.1A resolution.

Srivastava, D.B., Ethayathulla, A.S., Singh, N., Sharma, S., 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: 41.13 kDa 
• Atom Count: 3,147 
• Modeled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
signal processing protein	A	361	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q29411 (Sus scrofa) Explore Q29411  Go to UniProtKB:  Q29411
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	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.588	α = 90
b = 66.551	β = 90
c = 107.466	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: 2004-11-02 
Deposition Author(s): Srivastava, D.B., Ethayathulla, A.S., Singh, N., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2004-11-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 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