7JGM

Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with meta-benzenedihyrdoxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report



Literature

Tunable and Cooperative Thermomechanical Properties of Protein-Metal-Organic Frameworks.

Bailey, J.B.Tezcan, F.A.

(2020) J Am Chem Soc 

  • DOI: 10.1021/jacs.0c07835
  • Primary Citation of Related Structures:  
    7JGN, 7JGO, 7JGL, 7JGM, 7JGP, 7JGQ, 7JGK

  • PubMed Abstract: 
  • We recently introduced protein-metal-organic frameworks (protein-MOFs) as chemically designed protein crystals, composed of ferritin nodes that predictably assemble into 3D lattices upon coordination of various metal ions and ditopic, hydroxamate-bas ...

    We recently introduced protein-metal-organic frameworks (protein-MOFs) as chemically designed protein crystals, composed of ferritin nodes that predictably assemble into 3D lattices upon coordination of various metal ions and ditopic, hydroxamate-based linkers. Owing to their unique tripartite construction, protein-MOFs possess extremely sparse lattice connectivity, suggesting that they might display unusual thermomechanical properties. Leveraging the synthetic modularity of ferritin-MOFs, we investigated the temperature-dependent structural dynamics of six distinct frameworks. Our results show that the thermostabilities of ferritin-MOFs can be tuned through the metal component or the presence of crowding agents. Our studies also reveal a framework that undergoes a reversible and isotropic first-order phase transition near-room temperature, corresponding to a 4% volumetric change within 1 °C and a hysteresis window of ∼10 °C. This highly cooperative crystal-to-crystal transformation, which stems from the soft crystallinity of ferritin-MOFs, illustrates the advantage of modular construction strategies in discovering tunable-and unpredictable-material properties.


    Organizational Affiliation

    Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin heavy chainABCDEFGHIJKLMNOPQRSTUVWXabcdefghijklmnopqrstuvwx182Homo sapiensMutation(s): 5 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
NIH Common Fund Data Resources
PHAROS  P02794
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V9D
Query on V9D

Download CCD File 
F, I, R, W, a, j, n, t
N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide
C8 H8 N2 O4
OGCHBHAGINIXOG-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, D, G, J, M, P, S, V, a, d, g, j, m, p, t, v
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.55α = 90
b = 213.75β = 90.048
c = 155.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0003844

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release