7JGN

Crystal Structure of the Zn-bound Human Heavy-chain variant 122H-delta C-star with meta-benzenedihyrdoxamate collected at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


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
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 
BD [auth Q],
EB [auth B],
IC [auth K],
KD [auth T],
OB [auth E],
BD [auth Q],
EB [auth B],
IC [auth K],
KD [auth T],
OB [auth E],
UC [auth O],
VD [auth X],
ZB [auth H]
N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide
C8 H8 N2 O4
OGCHBHAGINIXOG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AC [auth I],
AD [auth Q],
AE [auth b],
AG [auth t],
BB [auth B],
AC [auth I],
AD [auth Q],
AE [auth b],
AG [auth t],
BB [auth B],
BC [auth I],
BE [auth b],
BF [auth k],
BG [auth u],
CB [auth B],
CC [auth J],
CD [auth R],
CE [auth c],
CF [auth k],
CG [auth u],
DB [auth B],
DC [auth J],
DD [auth R],
DE [auth c],
DF [auth l],
DG [auth v],
EC [auth J],
ED [auth S],
EE [auth d],
EF [auth l],
EG [auth v],
FB [auth C],
FD [auth S],
FE [auth d],
FF [auth m],
FG [auth v],
GB [auth C],
GC [auth K],
GD [auth S],
GE [auth d],
GF [auth m],
GG [auth v],
HB [auth C],
HC [auth K],
HE [auth d],
HF [auth m],
IB [auth D],
ID [auth T],
IG [auth w],
JB [auth D],
JC [auth L],
JD [auth T],
JE [auth e],
JF [auth n],
JG [auth w],
KB [auth D],
KC [auth L],
KE [auth e],
KF [auth n],
KG [auth w],
LC [auth M],
LD [auth U],
LE [auth e],
LF [auth o],
LG [auth x],
MB [auth E],
MC [auth M],
MD [auth U],
ME [auth f],
MF [auth o],
MG [auth x],
NB [auth E],
ND [auth V],
NE [auth f],
NF [auth p],
NG [auth x],
OC [auth N],
OD [auth V],
OE [auth f],
OF [auth p],
PB [auth F],
PC [auth N],
PE [auth g],
QB [auth F],
QC [auth O],
QD [auth W],
QE [auth g],
QF [auth q],
RB [auth F],
RC [auth O],
RD [auth W],
RE [auth g],
RF [auth q],
SB [auth G],
SC [auth O],
SD [auth X],
SF [auth q],
TB [auth G],
TC [auth O],
TD [auth X],
TE [auth h],
TF [auth r],
UB [auth G],
UD [auth X],
UE [auth h],
UF [auth r],
VC [auth P],
VE [auth i],
VF [auth s],
WA [auth A],
WB [auth H],
WC [auth P],
WD [auth a],
WE [auth i],
WF [auth s],
XA [auth A],
XB [auth H],
XC [auth P],
XD [auth a],
XE [auth j],
YA [auth A],
YB [auth H],
YD [auth a],
YE [auth j],
YF [auth t],
ZA [auth A],
ZC [auth Q],
ZE [auth j],
ZF [auth t]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AB [auth A],
AF [auth j],
FC [auth J],
HD [auth S],
HG [auth v],
AB [auth A],
AF [auth j],
FC [auth J],
HD [auth S],
HG [auth v],
IE [auth d],
IF [auth m],
LB [auth D],
NC [auth M],
PD [auth V],
PF [auth p],
SE [auth g],
VB [auth G],
XF [auth s],
YC [auth P],
ZD [auth a]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.75α = 90
b = 215.46β = 89.952
c = 156.46γ = 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