PDBsum entry 2q4d

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protein ligands Protein-protein interface(s) links
Structural genomics, unknown function PDB id
Protein chains
184 a.a. *
EDO ×4
Waters ×319
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene a
Structure: Lysine decarboxylase-like protein at5g11950. Chain: a, b. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Strain: cv. Columbia. Gene: at5g11950, f14f18.120. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.15Å     R-factor:   0.152     R-free:   0.207
Ensemble: 16 models
Authors: E.J.Levin,D.A.Kondrashov,G.E.Wesenberg,G.N.Phillips Jr.,Cent Eukaryotic Structural Genomics (Cesg)
Key ref:
E.J.Levin et al. (2007). Ensemble refinement of protein crystal structures: validation and application. Structure, 15, 1040-1052. PubMed id: 17850744 DOI: 10.1016/j.str.2007.06.019
31-May-07     Release date:   19-Jun-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q84MC2  (LOG8_ARATH) -  Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG8
216 a.a.
184 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.2  - Uridine nucleosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Uridine + H2O = D-ribose + uracil
+ H(2)O
= D-ribose
+ uracil
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     cytokinin biosynthetic process   1 term 
  Biochemical function     hydrolase activity     3 terms  


DOI no: 10.1016/j.str.2007.06.019 Structure 15:1040-1052 (2007)
PubMed id: 17850744  
Ensemble refinement of protein crystal structures: validation and application.
E.J.Levin, D.A.Kondrashov, G.E.Wesenberg, G.N.Phillips.
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.
  Selected figure(s)  
Figure 2.
Figure 2. Examples of Anharmonic Residue Probability Distributions for the Simulated Single- and Multiple-Conformer Models
The panels on the left show images of the electron density maps generated from the MD simulations of 1Q4R, along with a stick representation of the final 16-conformer model. The panels on the right show, for the red residues, the histograms of the projections of the simulation coordinates along the first principal components (shown in black), as well as the probability density functions calculated from the 1-conformer (red) and 16-conformer (blue) models along the same axis.
Figure 6.
Figure 6. Effect of Observation-to-Parameter Ratio on the Improvement in R[free] from Ensemble Refinement
The decrease in the R[free] value between the initial R[free] value and the R[free] value of the best-performing multiple-conformer model for the 50 experimental structures is plotted as a function of the ratio of the number of reflections used in the refinement to the number of atoms in the original one-conformer structure.
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 1040-1052) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21190057 J.S.Fraser, and C.J.Jackson (2011).
Mining electron density for functionally relevant protein polysterism in crystal structures.
  Cell Mol Life Sci, 68, 1829-1841.  
20669241 A.L.Stamp, P.Owen, K.E.Omari, C.E.Nichols, M.Lockyer, H.K.Lamb, I.G.Charles, A.R.Hawkins, and D.K.Stammers (2010).
Structural and functional characterization of Salmonella enterica serovar Typhimurium YcbL: an unusual Type II glyoxalase.
  Protein Sci, 19, 1897-1905.
PDB code: 2xf4
  20944235 B.Mohanty, P.Serrano, B.Pedrini, K.Jaudzems, M.Geralt, R.Horst, T.Herrmann, M.A.Elsliger, I.A.Wilson, and K.Wüthrich (2010).
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1381-1392.
PDB codes: 2k9z 2ka0
20973973 B.U.Klink, and A.J.Scheidig (2010).
New insight into the dynamic properties and the active site architecture of H-Ras p21 revealed by X-ray crystallography at very high resolution.
  BMC Struct Biol, 10, 38.  
20823548 E.Pozharski (2010).
Percentile-based spread: a more accurate way to compare crystallographic models.
  Acta Crystallogr D Biol Crystallogr, 66, 970-978.  
  20865158 J.E.Kohn, P.V.Afonine, J.Z.Ruscio, P.D.Adams, and T.Head-Gordon (2010).
Evidence of functional protein dynamics from X-ray crystallographic ensembles.
  PLoS Comput Biol, 6, 0.  
  21293729 K.Sikic, S.Tomic, and O.Carugo (2010).
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
  Open Biochem J, 4, 83-95.  
20499387 P.T.Lang, H.L.Ng, J.S.Fraser, J.E.Corn, N.Echols, M.Sales, J.M.Holton, and T.Alber (2010).
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
  Protein Sci, 19, 1420-1431.  
20648263 P.V.Afonine, R.W.Grosse-Kunstleve, V.B.Chen, J.J.Headd, N.W.Moriarty, J.S.Richardson, D.C.Richardson, A.Urzhumtsev, P.H.Zwart, and P.D.Adams (2010).
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.
  J Appl Crystallogr, 43, 669-676.  
20195256 S.I.O'Donoghue, D.S.Goodsell, A.S.Frangakis, F.Jossinet, R.A.Laskowski, M.Nilges, H.R.Saibil, A.Schafferhans, R.C.Wade, E.Westhof, and A.J.Olson (2010).
Visualization of macromolecular structures.
  Nat Methods, 7, S42-S55.  
19706521 A.Bakan, and I.Bahar (2009).
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding.
  Proc Natl Acad Sci U S A, 106, 14349-14354.  
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
19602499 B.Savić, S.Tomić, V.Magnus, K.Gruden, K.Barle, R.Grenković, J.Ludwig-Müller, and B.Salopek-Sondi (2009).
Auxin amidohydrolases from Brassica rapa cleave the alanine conjugate of indolepropionic acid as a preferable substrate: a biochemical and modeling approach.
  Plant Cell Physiol, 50, 1587-1599.  
19167297 D.Riccardi, Q.Cui, and G.N.Phillips (2009).
Application of elastic network models to proteins in the crystalline state.
  Biophys J, 96, 464-475.  
19905144 F.R.Maia, T.Ekeberg, N.Tîmneanu, D.van der Spoel, and J.Hajdu (2009).
Structural variability and the incoherent addition of scattered intensities in single-particle diffraction.
  Phys Rev E Stat Nonlin Soft Matter Phys, 80, 031905.  
19770508 H.van den Bedem, A.Dhanik, J.C.Latombe, and A.M.Deacon (2009).
Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers.
  Acta Crystallogr D Biol Crystallogr, 65, 1107-1117.  
19130299 J.L.Markley, D.J.Aceti, C.A.Bingman, B.G.Fox, R.O.Frederick, S.Makino, K.W.Nichols, G.N.Phillips, J.G.Primm, S.C.Sahu, F.C.Vojtik, B.F.Volkman, R.L.Wrobel, and Z.Zolnai (2009).
The Center for Eukaryotic Structural Genomics.
  J Struct Funct Genomics, 10, 165-179.  
19145244 K.Lindorff-Larsen, and J.Ferkinghoff-Borg (2009).
Similarity measures for protein ensembles.
  PLoS ONE, 4, e4203.  
19688820 L.Liu, L.M.Koharudin, A.M.Gronenborn, and I.Bahar (2009).
A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations.
  Proteins, 77, 927-939.  
19127591 L.Yang, G.Song, and R.L.Jernigan (2009).
Comparisons of experimental and computed protein anisotropic temperature factors.
  Proteins, 76, 164-175.  
19553204 P.V.Burra, Y.Zhang, A.Godzik, and B.Stec (2009).
Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure.
  Proc Natl Acad Sci U S A, 106, 10505-10510.  
18300241 B.D.Sellers, K.Zhu, S.Zhao, R.A.Friesner, and M.P.Jacobson (2008).
Toward better refinement of comparative models: predicting loops in inexact environments.
  Proteins, 72, 959-971.  
18588493 C.D.Snow (2008).
Hunting for predictive computational drug-discovery models.
  Expert Rev Anti Infect Ther, 6, 291-293.  
18391405 J.L.Knight, Z.Zhou, E.Gallicchio, D.M.Himmel, R.A.Friesner, E.Arnold, and R.M.Levy (2008).
Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.
  Acta Crystallogr D Biol Crystallogr, 64, 383-396.  
18094466 M.Delarue (2008).
Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis.
  Acta Crystallogr D Biol Crystallogr, 64, 40-48.  
18989041 P.Yao, A.Dhanik, N.Marz, R.Propper, C.Kou, G.Liu, H.van den Bedem, J.C.Latombe, I.Halperin-Landsberg, and R.B.Altman (2008).
Efficient algorithms to explore conformation spaces of flexible protein loops.
  IEEE/ACM Trans Comput Biol Bioinform, 5, 534-545.  
18462683 R.C.Page, S.Kim, and T.A.Cross (2008).
Transmembrane helix uniformity examined by spectral mapping of torsion angles.
  Structure, 16, 787-797.  
17965015 C.M.Bianchetti, L.Yi, S.W.Ragsdale, and G.N.Phillips (2007).
Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2.
  J Biol Chem, 282, 37624-37631.
PDB codes: 2q32 2qpp 2rgz
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.