3P96

Crystal structure of Phosphoserine phosphatase SerB from Mycobacterium avium, native form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

SAD phasing using iodide ions in a high-throughput structural genomics environment.

Abendroth, J.Gardberg, A.S.Robinson, J.I.Christensen, J.S.Staker, B.L.Myler, P.J.Stewart, L.J.Edwards, T.E.

(2011) J Struct Funct Genomics 12: 83-95

  • DOI: 10.1007/s10969-011-9101-7
  • Primary Citation of Related Structures:  
    3K9G, 3KM3, 3KW3, 3NJB, 3OIB, 3O2E, 3PFD, 3PM6, 3MEN, 3LUZ

  • PubMed Abstract: 
  • The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures ...

    The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.


    Related Citations: 
    • Increasing the structural coverage of tuberculosis drug targets.
      Baugh, L., Phan, I., Begley, D.W., Clifton, M.C., Armour, B., Dranow, D.M., Taylor, B.M., Muruthi, M.M., Abendroth, J., Fairman, J.W., Fox, D., Dieterich, S.H., Staker, B.L., Gardberg, A.S., Choi, R., Hewitt, S.N., Napuli, A.J., Myers, J., Barrett, L.K., Zhang, Y., Ferrell, M., Mundt, E., Thompkins, K., Tran, N., Lyons-Abbott, S., Abramov, A., Sekar, A., Serbzhinskiy, D., Lorimer, D., Buchko, G.W., Stacy, R., Stewart, L.J., Edwards, T.E., Van Voorhis, W.C., Myler, P.J.
      (2014) Tuberculosis (Edinb) --: --

    Organizational Affiliation

    Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoserine phosphatase SerB A415Mycobacterium avium 104Mutation(s): 0 
Gene Names: serBMAV_3907
EC: 3.1.3.3
Find proteins for A0QJI1 (Mycobacterium avium (strain 104))
Explore A0QJI1 
Go to UniProtKB:  A0QJI1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.53α = 90
b = 109.19β = 90
c = 134.32γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-03-11
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description