5KCI

Crystal Structure of HTC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.833 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Determining crystal structures through crowdsourcing and coursework.

Horowitz, S.Koepnick, B.Martin, R.Tymieniecki, A.Winburn, A.A.Cooper, S.Flatten, J.Rogawski, D.S.Koropatkin, N.M.Hailu, T.T.Jain, N.Koldewey, P.Ahlstrom, L.S.Chapman, M.R.Sikkema, A.P.Skiba, M.A.Maloney, F.P.Beinlich, F.R.Popovic, Z.Baker, D.Khatib, F.Bardwell, J.C.

(2016) Nat Commun 7: 12549-12549

  • DOI: 10.1038/ncomms12549

  • PubMed Abstract: 
  • We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulne ...

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.


    Organizational Affiliation

    Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.,Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, USA.,Program in Cognitive Science, Indiana University, 1900 E 10th Street, Bloomington, Indiana 47406, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Computer Science and Engineering, Center for Game Science, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.,ProQR Therapeutics NV., 2333 Leiden, The Netherlands.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Center for Complex Networks and Systems Research, Department of Informatics, Indiana University, Bloomington, Indiana 47408, USA.,Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum, D-52428 J├╝lich, Germany.,Northeastern University, College of Computer and Information Science, Boston, Massachusetts 02115, USA.,Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, Massachusetts 02747, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YPL067C
A
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Find proteins for Q02754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02754
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.833 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.460α = 90.00
b = 62.460β = 90.00
c = 117.580γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM102829

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-11-01
    Type: Author supporting evidence