2D6B

Novel Bromate Species trapped within a Protein Crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

An ensemble of crystallographic models enables the description of novel bromate-oxoanion species trapped within a protein crystal

Ondracek, J.Mesters, J.R.

(2006) Acta Crystallogr D Biol Crystallogr 62: 996-1001

  • DOI: 10.1107/S0907444906021627
  • Primary Citation of Related Structures:  
    2D6B

  • PubMed Abstract: 
  • Only a few protein-oxoanion crystal complexes have been described to date. Here, the structure of a protein soaked in a bromate solution has been determined to a resolution of 1.25 A and refined to final overall R/R(free) values of 18.04/21.3 (isotro ...

    Only a few protein-oxoanion crystal complexes have been described to date. Here, the structure of a protein soaked in a bromate solution has been determined to a resolution of 1.25 A and refined to final overall R/R(free) values of 18.04/21.3 (isotropic) and 11.25/14.67 (anisotropic). In contrast to the single-model approach, refinement of an ensemble of ten models enabled us to determine variances and statistically evaluate bond-length distances and angles in the oxoanions. In total, nine bromate positions, including two BrO(3)(-) x HBrO(3) dimer species, have been identified on the basis of the anomalous signal of the Br atoms. For all bromate ions, the main-chain amide atoms of the protein were identified as the dominant binding positions, a useful property in any experimental phase-determination experiment.


    Organizational Affiliation

    Department of Recombinant Expression and Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, CZ-16637 Praha 6, Czech Republic. ondracek@img.cas.cz



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
202
Query on 202

Download CCD File 
A
BROMIC ACID
Br H O3
SXDBWCPKPHAZSM-QEZKKOIZCW
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.21α = 90
b = 77.21β = 90
c = 38.191γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CCP4model building
HipHoprefinement
CCP4phasing
SHELXLrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-09-09
    Changes: Version format compliance
  • Version 1.4: 2017-10-11
    Changes: Refinement description