1VLR | pdb_00001vlr

Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VLR/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-10 Released: 2004-08-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.201 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution.

Han, G.W., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Axelrod, H., Biorac, T., Canaves, J.M., Chiu, H.J., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Haugen, J., Hornsby, M., Jaroszewski, L., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., McPhillips, T.M., Miller, M.D., Moy, K., Nigoghossian, E., Paulsen, J., Quijano, K., Reyes, R., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2005) Proteins 60: 797-802

• PubMed: 16001405 
• DOI: https://doi.org/10.1002/prot.20467
• Primary Citation Related Structures: 
  1VLR

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Organizational Affiliation: 
• Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

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)

Macromolecule Content 

• Total Structure Weight: 81.38 kDa 
• Atom Count: 5,721 
• Modeled Residue Count: 582 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA decapping enzyme	A, B	350	Mus musculus	Mutation(s): 0  Gene Names: DcpS EC: 3.6.1.59
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DAR7 (Mus musculus) Explore Q9DAR7  Go to UniProtKB:  Q9DAR7
IMPC:  MGI:1916555

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.201 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VLR

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.399	α = 90
b = 59.231	β = 103.8
c = 100.14	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-08-24
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description