2Q4X

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2F2G - determined by Wesenberg, G.W., Smith, D.W., Phillips Jr., G.N., Johnson, K.A., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)  

Literature

Ensemble refinement of protein crystal structures: validation and application.

Levin, E.J.Kondrashov, D.A.Wesenberg, G.E.Phillips, G.N.

(2007) Structure 15: 1040-1052

  • DOI: 10.1016/j.str.2007.06.019
  • Primary Citation of Related Structures:  
    2Q52, 2Q51, 2Q50, 2Q4Z, 2Q4Y, 2Q4V, 2Q4U, 2Q4T, 2Q4S, 2Q4R, 2Q4Q, 2Q4P, 2Q4O, 2Q4N, 2Q4M, 2Q4L, 2Q4K, 2Q4J, 2Q4I, 2Q4H, 2Q4F, 2Q4E, 2Q4D, 2Q4C, 2Q4B, 2Q49, 2Q4A, 2Q48, 2Q47, 2Q46, 2Q45, 2Q44, 2Q43, 2Q42, 2Q41, 2Q40, 2Q3W, 2Q3V, 2Q3U, 2Q3T, 2Q3S, 2Q3R, 2Q3Q, 2Q3P, 2Q3O, 2Q3M
  • Also Cited By: 2Q53, 2Q4W, 2Q4G

  • PubMed Abstract: 
  • X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of repre ...

    X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.


    Related Citations: 
    • Crystal structure of gene locus At3g16990 from Arabidopsis thaliana
      Blommel, P.G.,Smith, D.W.,Bingman, C.A.,Dyer, D.H.,Rayment, I.,Holden, H.M.,Fox, B.G.,Phillips Jr., G.N.
      (2004) Proteins 57: 221


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seed maturation protein PM36 homolog
A, B
221Arabidopsis thalianaMutation(s): 1 
Gene Names: TENA_E
EC: 3.5.1.-, 3.5.99.2
Find proteins for Q9ASY9 (Arabidopsis thaliana)
Go to UniProtKB:  Q9ASY9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HMH
Query on HMH

Download SDF File 
Download CCD File 
A, B
4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
C6 H9 N3 O
VUTBELPREDJDDH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.136 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.700α = 90.00
b = 62.700β = 90.00
c = 287.621γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2007-09-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-08-10
    Type: Other