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 

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.Genom. 12: 83-95

  • DOI: 10.1007/s10969-011-9101-7
  • Primary Citation of Related Structures:  
  • Also Cited By: 5JMA, 5JLR, 5JLP, 5JJB, 5IT4, 5IT0, 5IS2

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoserine phosphatase SerB
A
415Mycobacterium avium (strain 104)Mutation(s): 0 
Gene Names: serB
EC: 3.1.3.3
Find proteins for A0QJI1 (Mycobacterium avium (strain 104))
Go to UniProtKB:  A0QJI1
Small Molecules
Ligands 3 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
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 65.530α = 90.00
b = 109.190β = 90.00
c = 134.320γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHENIXphasing
ADSCdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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