2EG9 | pdb_00002eg9

Crystal structure of the truncated extracellular domain of mouse CD38

• PDB DOI: https://doi.org/10.2210/pdb2EG9/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2007-02-28 Released: 2008-03-11 
• Deposition Author(s): Kukimoto-Niino, M., Mishima, C., Wakiyama, M., Terada, T., Shirouzu, M., Hara-Yokoyama, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.340 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the truncated extracellular domain of mouse CD38

Kukimoto-Niino, M., Mishima, C., Wakiyama, M., Terada, T., Shirouzu, M., Hara-Yokoyama, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.3 kDa 
• Atom Count: 3,412 
• Modeled Residue Count: 424 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase 1	A, B	253	Mus musculus	Mutation(s): 4  Gene Names: Cd38 EC: 3.2.2.5 (PDB Primary Data), 3.2.2 (UniProt), 3.2.2.6 (UniProt), 2.4.99.20 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P56528 (Mus musculus) Explore P56528  Go to UniProtKB:  P56528
IMPC:  MGI:107474

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.340 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.072	α = 90
b = 176.815	β = 90
c = 44.573	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Kukimoto-Niino, M., Mishima, C., Wakiyama, M., Terada, T., Shirouzu, M., Hara-Yokoyama, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary