4TKQ | pdb_00004tkq

Native-SAD phasing for YetJ from Bacillus Subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.260 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4TKQ

This is version 1.5 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 D Biol Crystallogr 70: 2544-2557

  • DOI: https://doi.org/10.1107/S1399004714013376
  • Primary Citation Related Structures: 
    4TKQ, 4TKR, 4TKS

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 24.26 kDa 
  • Atom Count: 1,636 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 217 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein YetJ217Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yetJBSU07200
Membrane Entity: Yes 
UniProt
Find proteins for O31539 (Bacillus subtilis (strain 168))
Explore O31539 
Go to UniProtKB:  O31539
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31539
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.260 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.869α = 90
b = 61.869β = 90
c = 288.401γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095315

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2014-10-22
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Refinement description