3E78

Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37.

Sippel, K.H.Robbins, A.H.Reutzel, R.Domsic, J.Boehlein, S.K.Govindasamy, L.Agbandje-McKenna, M.Rosser, C.J.McKenna, R.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1172-1178

  • DOI: 10.1107/S0907444908030175
  • Primary Citation of Related Structures:  
    3E78, 3E79

  • PubMed Abstract: 
  • The crystal structure of the Mycoplasma hyorhinis protein Mh-p37 has been solved and refined to 1.9 A resolution. This is the first de novo structure to be determined using the recently described heavy-atom reagent [Beck et al. (2008), Acta Cryst. D6 ...

    The crystal structure of the Mycoplasma hyorhinis protein Mh-p37 has been solved and refined to 1.9 A resolution. This is the first de novo structure to be determined using the recently described heavy-atom reagent [Beck et al. (2008), Acta Cryst. D64, 1179-1182] 5-amino-2,4,6-triiodoisophthalic acid (I3C), which contains three I atoms arranged in an equilateral triangle, by SIRAS methods. Data collection was performed in-house at room temperature. SHELXD and SHELXE were used to determine the I-atom positions and phase the native protein and PHENIX AutoBuild software was used to automatically fit the amino-acid sequence to the electron-density map. The structure was refined using SHELX97 to an R(cryst) of 18.6% and an R(free) of 24.0%. Mh-p37 is an alpha/beta protein with two well defined domains which are separated by a deep cleft. An unanticipated ligand bound in the center of the molecule at the base of the cleft has been modeled as thiamine pyrophosphate or vitamin B(1). Retrospective attempts to solve the crystal structure by Patterson search methods using either isomorphous or anomalous differences failed. Additionally, attempts to use proteins with the highest structural homology in the Protein Data Bank to phase the data by molecular replacement were unsuccessful, most likely in hindsight because of their poor structural agreement. Therefore, the I3C reagent offers an alternative, quick and inexpensive method for in-house phasing of de novo structures where other methods may not be successful.


    Related Citations: 
    • A magic triangle for experimental phasing of macromolecules
      Beck, T., Krasauskas, A., Gruene, T., Sheldrick, G.M.
      () To be published --: --

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity transport system protein p37A403Mycoplasma hyorhinisMutation(s): 0 
Gene Names: p37
Find proteins for P15363 (Mycoplasma hyorhinis)
Explore P15363 
Go to UniProtKB:  P15363
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download CCD File 
A
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.445α = 90
b = 68.761β = 108.04
c = 60.024γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
SHELXEmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance