2IAY

Crystal structure of a duf1831 family protein (lp2179) from lactobacillus plantarum at 1.20 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism.

Bakolitsa, C.Kumar, A.Carlton, D.Miller, M.D.Krishna, S.S.Abdubek, P.Astakhova, T.Axelrod, H.L.Chiu, H.J.Clayton, T.Deller, M.C.Duan, L.Elsliger, M.A.Feuerhelm, J.Grzechnik, S.K.Grant, J.C.Han, G.W.Jaroszewski, L.Jin, K.K.Klock, H.E.Knuth, M.W.Kozbial, P.Marciano, D.McMullan, D.Morse, A.T.Nigoghossian, E.Okach, L.Oommachen, S.Paulsen, J.Reyes, R.Rife, C.L.Tien, H.J.Trout, C.V.van den Bedem, H.Weekes, D.Xu, Q.Hodgson, K.O.Wooley, J.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2010) Acta Crystallogr.,Sect.F 66: 1205-1210

  • DOI: 10.1107/S1744309109023689

  • PubMed Abstract: 
  • The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests a novel α+β fold comprising two β-sheets packed against a single helix. A remote structural similarity to two other uncharacterized protein families specific to the Bacillus ...

    The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests a novel α+β fold comprising two β-sheets packed against a single helix. A remote structural similarity to two other uncharacterized protein families specific to the Bacillus genus (PF08868 and PF08968), as well as to prokaryotic S-adenosylmethionine decarboxylases, is consistent with a role in amino-acid metabolism. Genomic neighborhood analysis of LP2179 supports this functional assignment, which might also then be extended to PF08868 and PF08968.


    Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein
A
114Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)N/A
Find proteins for F9UQB2 (Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Go to UniProtKB:  F9UQB2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 36.289α = 90.00
b = 47.896β = 90.00
c = 58.010γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling
PDB_EXTRACTdata extraction
SOLVEphasing
MolProbitymodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description