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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

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

(2020) J Am Chem Soc 142: 17265-17270

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

  • 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-based linkers ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin heavy chain
A,
B,
C,
D,
E,
182Homo sapiensMutation(s): 5 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
GTEx:  ENSG00000167996 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V9D (Subject of Investigation/LOI)
Query on V9D

Download Ideal Coordinates CCD File 
IC [auth R],
IE [auth t],
KB [auth F],
QD [auth j],
RB [auth I],
IC [auth R],
IE [auth t],
KB [auth F],
QD [auth j],
RB [auth I],
RC [auth W],
XC [auth a],
XD [auth n]
N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide
C8 H8 N2 O4
OGCHBHAGINIXOG-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
AB [auth B],
AC [auth N],
AD [auth d],
AE [auth p],
BB [auth B],
AB [auth B],
AC [auth N],
AD [auth d],
AE [auth p],
BB [auth B],
BC [auth O],
BD [auth d],
CB [auth C],
CC [auth O],
CD [auth d],
CE [auth q],
DB [auth C],
DC [auth P],
DE [auth r],
EB [auth D],
EC [auth P],
ED [auth e],
EE [auth s],
FB [auth D],
FD [auth e],
FE [auth t],
GC [auth Q],
GD [auth f],
GE [auth t],
HB [auth E],
HC [auth R],
HD [auth f],
IB [auth F],
ID [auth g],
JB [auth F],
JC [auth S],
JD [auth g],
JE [auth u],
KC [auth S],
KE [auth v],
LB [auth G],
LD [auth h],
LE [auth v],
MB [auth G],
MC [auth T],
MD [auth i],
ME [auth v],
NC [auth U],
ND [auth j],
OB [auth H],
OC [auth V],
OD [auth j],
OE [auth w],
PB [auth H],
PE [auth w],
QB [auth I],
QC [auth W],
QE [auth x],
RD [auth k],
RE [auth x],
SB [auth J],
SC [auth X],
SD [auth l],
TC [auth X],
TD [auth m],
UB [auth K],
UC [auth a],
UD [auth m],
VB [auth L],
VC [auth a],
WA [auth A],
WB [auth L],
WD [auth n],
XA [auth A],
XB [auth M],
YB [auth M],
YC [auth b],
YD [auth o],
ZA [auth B],
ZC [auth c],
ZD [auth p]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BE [auth p],
DD [auth d],
FC [auth P],
GB [auth D],
HE [auth t],
BE [auth p],
DD [auth d],
FC [auth P],
GB [auth D],
HE [auth t],
KD [auth g],
LC [auth S],
NB [auth G],
NE [auth v],
PC [auth V],
PD [auth j],
TB [auth J],
VD [auth m],
WC [auth a],
YA [auth A],
ZB [auth M]
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



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references