4J9T

Crystal structure of a putative, de novo designed unnatural amino acid dependent metalloprotein, northeast structural genomics consortium target OR61


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy.

Mills, J.H.Khare, S.D.Bolduc, J.M.Forouhar, F.Mulligan, V.K.Lew, S.Seetharaman, J.Tong, L.Stoddard, B.L.Baker, D.

(2013) J.Am.Chem.Soc. 135: 13393-13399

  • DOI: 10.1021/ja403503m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation and the identities and orientations of surrounding residues represents a formidable chall ...

    Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation and the identities and orientations of surrounding residues represents a formidable challenge. Computational design methods have been used to identify optimal locations for functional sites in proteins and design the surrounding residues but have not incorporated unnatural amino acids in this process. We extended the Rosetta design methodology to design metalloproteins in which the amino acid (2,2'-bipyridin-5yl)alanine (Bpy-Ala) is a primary ligand of a bound metal ion. Following initial results that indicated the importance of buttressing the Bpy-Ala amino acid, we designed a buried metal binding site with octahedral coordination geometry consisting of Bpy-Ala, two protein-based metal ligands, and two metal-bound water molecules. Experimental characterization revealed a Bpy-Ala-mediated metalloprotein with the ability to bind divalent cations including Co(2+), Zn(2+), Fe(2+), and Ni(2+), with a Kd for Zn(2+) of ∼40 pM. X-ray crystal structures of the designed protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 Å respectively over all atoms in the binding site.


    Organizational Affiliation

    Department of Biochemistry and ⊥Biomolecular Structure and Design Program, University of Washington , Seattle, Washington, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
designed unnatural amino acid dependent metalloprotein
A
363Micromonospora viridifaciensMutations: S213D, W109F, I188F, A46D, A180T, H23I, H214E, S22R, E110A, A230R, D265N, H85D
Gene Names: nedA
EC: 3.2.1.18
Find proteins for Q02834 (Micromonospora viridifaciens)
Go to UniProtKB:  Q02834
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARS
Query on ARS

Download SDF File 
Download CCD File 
A
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.163α = 90.00
b = 79.677β = 90.00
c = 83.777γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
COMOphasing
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
ADSCdata collection
XTALVIEWrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-09-25
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description