5VEH

Re-refinement OF THE PDB STRUCTURE 1yiz of Aedes aegypti kynurenine aminotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:1yiz


Literature

Detect, correct, retract: How to manage incorrect structural models.

Wlodawer, A.Dauter, Z.Porebski, P.J.Minor, W.Stanfield, R.Jaskolski, M.Pozharski, E.Weichenberger, C.X.Rupp, B.

(2018) FEBS J 285: 444-466

  • DOI: 10.1111/febs.14320
  • Primary Citation of Related Structures:  
    5VEH, 5VEP, 5VEQ, 5VER, 5VET, 5VF2, 5VF5, 5VGA

  • PubMed Abstract: 
  • The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe ...

    The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees and editors? Once detected, what can be done to either correct, improve or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record.


    Related Citations: 
    • Crystal structures of Aedes aegypti kynurenine aminotransferase.
      Han, Q., Gao, Y.G., Robinson, H., Ding, H., Wilson, S., Li, J.
      (2005) FEBS J 272: 2198

    Organizational Affiliation

    Department of Genetic Epidemiology, Medical University Innsbruck, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kynurenine aminotransferaseA, B427Aedes aegyptiMutation(s): 0 
Gene Names: KAT5564787AAEL004435
EC: 2.6.1.63 (UniProt), 2.6.1.7 (UniProt), 4.4.1.13 (UniProt)
UniProt
Find proteins for Q17CS8 (Aedes aegypti)
Explore Q17CS8 
Go to UniProtKB:  Q17CS8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, BL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.288α = 90
b = 94.984β = 90
c = 167.599γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection