4JGJ | pdb_00004jgj

Crystal structure of the Ig-like D1 domain from mouse Carcinoembryogenic antigen-related cell adhesion molecule 15 (CEACAM15) [PSI-NYSGRC-005691]

• PDB DOI: https://doi.org/10.2210/pdb4JGJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-03-01 Released: 2013-03-13 
• Deposition Author(s): Kumar, P.R., Bonanno, J., Ahmed, M., Banu, R., Bhosle, R., Calarese, D., Celikigil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S., Glenn, A.S., Hillerich, B., Khafizov, K., Love, J., Patel, H., Seidel, R., Stead, M., Toro, R., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.222 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of the Ig-like D1 domain of CEACAM15 from Mus musculus [NYSGRC-005691]

Kumar, P.R., Bonanno, J., Nathenson, S.G., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.4 kDa 
• Atom Count: 1,788 
• Modeled Residue Count: 225 
• Deposited Residue Count: 268 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carcinoembryonic antigen-related cell adhesion molecule 15	A, B	126	Mus musculus	Mutation(s): 0  Gene Names: CEACAM-15, Ceacam15
UniProt
Find proteins for A0A0B4J1L0 (Mus musculus) Explore A0A0B4J1L0  Go to UniProtKB:  A0A0B4J1L0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown peptide	C [auth X], D [auth Y]	8	Mus musculus	Mutation(s): 0  Gene Names: CEACAM-15

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.222 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.168	α = 90
b = 101.168	β = 90
c = 75.729	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Kumar, P.R., Bonanno, J., Ahmed, M., Banu, R., Bhosle, R., Calarese, D., Celikigil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S., Glenn, A.S., Hillerich, B., Khafizov, K., Love, J., Patel, H., Seidel, R., Stead, M., Toro, R., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Structure summary