4TKQ

Native-SAD phasing for YetJ from Bacillus Subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8025 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Multi-crystal native SAD analysis at 6 keV.

Liu, Q.Guo, Y.Chang, Y.Cai, Z.Assur, Z.Mancia, F.Greene, M.I.Hendrickson, W.A.

(2014) Acta Crystallogr.,Sect.D 70: 2544-2557

  • DOI: 10.1107/S1399004714013376
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple ...

    Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.


    Organizational Affiliation

    NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YetJ
A
217Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yetJ
Find proteins for O31539 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31539
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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8025 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.221 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.869α = 90.00
b = 61.869β = 90.00
c = 288.401γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM095315

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references
  • Version 1.2: 2014-10-22
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Derived calculations, Other, Source and taxonomy