8YKR | pdb_00008ykr

Enhancing the Gastric Stability of Ferritin Nanocage via Computational-Assisted Disulfide Bond Engineering

PDB DOI: https://doi.org/10.2210/pdb8YKR/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Penaeus japonicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-03-05 Released: 2025-03-19
Deposition Author(s): Gu, C.K., Wang, S.J., Zhao, G.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Enhancing the Gastric Stability of Ferritin Nanocage via Computational-Assisted Disulfide Bond Engineering

Gu, C.K., Wang, S.J., Zhao, G.H.

To be published.

Macromolecule Content

Total Structure Weight: 117.23 kDa
Atom Count: 8,097
Modeled Residue Count: 1,006
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F	170	Penaeus japonicus	Mutation(s): 8 EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus) Explore T2B7E1 Go to UniProtKB: T2B7E1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T2B7E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth A] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth F] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain P [auth F]	G [auth B] H [auth B] I [auth A] J [auth C] K [auth D] G [auth B], H [auth B], I [auth A], J [auth C], K [auth D], L [auth D], M [auth E], N [auth E], O [auth F], P [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.230 (Depositor), 0.231 (DCC)
R-Value Work: 0.185 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.08	α = 90
b = 125.08	β = 90
c = 175.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32030084

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.