3BY7

CRYSTAL STRUCTURE OF A PROTEIN STRUCTURALLY SIMILAR TO SM/LSM-LIKE RNA-BINDING PROTEINS (JCVI_PEP_1096686650277) FROM UNCULTURED MARINE ORGANISM AT 2.60 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

Das, D.Kozbial, P.Axelrod, H.L.Miller, M.D.McMullan, D.Krishna, S.S.Abdubek, P.Acosta, C.Astakhova, T.Burra, P.Carlton, D.Chen, C.Chiu, H.J.Clayton, T.Deller, M.C.Duan, L.Elias, Y.Elsliger, M.A.Ernst, D.Farr, C.Feuerhelm, J.Grzechnik, A.Grzechnik, S.K.Hale, J.Han, G.W.Jaroszewski, L.Jin, K.K.Johnson, H.A.Klock, H.E.Knuth, M.W.Kumar, A.Marciano, D.Morse, A.T.Murphy, K.D.Nigoghossian, E.Nopakun, A.Okach, L.Oommachen, S.Paulsen, J.Puckett, C.Reyes, R.Rife, C.L.Sefcovic, N.Sudek, S.Tien, H.Trame, C.Trout, C.V.van den Bedem, H.Weekes, D.White, A.Xu, Q.Hodgson, K.O.Wooley, J.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2009) Proteins 75: 296-307

  • DOI: 10.1002/prot.22360

  • PubMed Abstract: 
  • ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity ...

    ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.


    Organizational Affiliation

    Joint Center for Structural Genomics, 2 Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
uncharacterized protein
A, B, C, D, E
100N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 108.250α = 90.00
b = 77.180β = 113.82
c = 71.470γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MAR345data collection
REFMACrefinement
XSCALEdata scaling
SHELXphasing
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
MolProbitymodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description