Native-SAD phasing for ThiT from Listeria monocytogenes serovar.

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 

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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 of 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiamine transporter thia
A, B
214Listeria monocytogenesMutation(s): 0 
Gene Names: M637_10125M638_09860M640_06115M641_06335M643_01630M644_08810M645_06650
Membrane Entity: Yes 
Find proteins for A0A0B8R2U7 (Listeria monocytogenes)
Explore A0A0B8R2U7 
Go to UniProtKB:  A0A0B8R2U7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B8R2U7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TPP

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
C12 H19 N4 O7 P2 S
Query on BGL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
C14 H28 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.647α = 90
b = 95.647β = 90
c = 125.027γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095315
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107462

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2014-10-08
    Changes: Database references
  • Version 1.3: 2014-10-22
    Changes: Database references
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 1.7: 2023-12-27
    Changes: Data collection, Database references, Structure summary