4W6T

Crystal Structure of Full-Length Split GFP Mutant E115H/T118H With Copper Mediated Crystal Contacts, P 43 21 2 Space Group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

A Suite of Engineered GFP Molecules for Oligomeric Scaffolding.

Leibly, D.J.Arbing, M.A.Pashkov, I.DeVore, N.Waldo, G.S.Terwilliger, T.C.Yeates, T.O.

(2015) Structure 23: 1754-1768

  • DOI: https://doi.org/10.1016/j.str.2015.07.008
  • Primary Citation of Related Structures:  
    4W69, 4W6A, 4W6B, 4W6C, 4W6D, 4W6F, 4W6G, 4W6H, 4W6I, 4W6J, 4W6K, 4W6L, 4W6M, 4W6N, 4W6O, 4W6P, 4W6R, 4W6S, 4W6T, 4W6U, 4W72, 4W73, 4W74, 4W75, 4W76, 4W77, 4W7A, 4W7C, 4W7D, 4W7E, 4W7F, 4W7R, 4W7X

  • PubMed Abstract: 

    Applications ranging from synthetic biology to protein crystallization could be advanced by facile systems for connecting multiple proteins together in predefined spatial relationships. One approach to this goal is to engineer many distinct assembly forms of a single carrier protein or scaffold, to which other proteins of interest can then be readily attached. In this work we chose GFP as a scaffold and engineered many alternative oligomeric forms, driven by either specific disulfide bond formation or metal ion addition. We generated a wide range of spatial arrangements of GFP subunits from 11 different oligomeric variants, and determined their X-ray structures in a total of 33 distinct crystal forms. Some of the oligomeric GFP variants show geometric polymorphism depending on conditions, while others show considerable geometric rigidity. Potential future applications of this system are discussed.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
fluorescent protein E115H/T118H229synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
O [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.3α = 90
b = 105.3β = 90
c = 69.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098177

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection
  • Version 1.6: 2024-11-06
    Changes: Structure summary