5JKL

Binary crystal structure of positively and negatively supercharged variants Ftn(pos) and Ftn(neg) from human heavy chain ferritin (Mg formate condition)

PDB DOI: https://doi.org/10.2210/pdb5JKL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-04-26 Released: 2016-10-26
Deposition Author(s): Kuenzle, M., Beck, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.176
R-Value Work: 0.147
R-Value Observed: 0.148

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Binary Protein Crystals for the Assembly of Inorganic Nanoparticle Superlattices.

Kunzle, M., Eckert, T., Beck, T.

(2016) J Am Chem Soc 138: 12731-12734

PubMed: 27617514 Search on PubMed
DOI: https://doi.org/10.1021/jacs.6b07260
Primary Citation of Related Structures:
5JKL, 5JKM

PubMed Abstract:
Biomolecules can act as functional templates for the organization of inorganic particles. Here we use two protein containers, engineered with opposite surface charge, as building blocks for the construction of a new type of biohybrid material. Binary structures with crystalline order were obtained, adopting a tetragonal lattice. Moreover, the cavity of the engineered protein containers can be filled with inorganic nanoparticles. The controlled assembly of these protein-nanoparticle composites yields highly ordered binary nanoparticle superlattices as free-standing crystals, with up to a few hundred micrometers in size. Because the structure and lattice parameters of the protein-nanoparticle crystals are independent of their nanoparticle cargo, the binary protein material may serve as a generally applicable matrix for the assembly of a variety of nanoparticles types.

Organizational Affiliation

Institute of Inorganic Chemistry, RWTH Aachen University , 52074 Aachen, Germany.

Macromolecule Content

Total Structure Weight: 258.96 kDa
Atom Count: 18,527
Modelled Residue Count: 2,064
Deposited Residue Count: 2,196
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	A, B, C, D, E A, B, C, D, E, F	183	Homo sapiens	Mutation(s): 10 Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02794
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	G, H, I, J, K G, H, I, J, K, L	183	Homo sapiens	Mutation(s): 5 Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02794
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain T [auth B] SDF format, chain W [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] mmCIF format, chain EA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C]	EA [auth E], T [auth B], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain T [auth B] Focus chain W [auth C] Interactions & Density Focus chain EA [auth E] Focus chain T [auth B] Focus chain W [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain R [auth B] SDF format, chain SA [auth I] SDF format, chain TA [auth J] SDF format, chain U [auth C] SDF format, chain VA [auth K] SDF format, chain X [auth D] SDF format, chain XA [auth L] SDF format, chain Y [auth D] SDF format, chain YA [auth L] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain TA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain VA [auth K] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth L] mmCIF format, chain CA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain PA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth I] mmCIF format, chain TA [auth J] mmCIF format, chain U [auth C] mmCIF format, chain VA [auth K] mmCIF format, chain X [auth D] mmCIF format, chain XA [auth L] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth L]	CA [auth E] FA [auth F] GA [auth F] JA [auth G] KA [auth G] CA [auth E], FA [auth F], GA [auth F], JA [auth G], KA [auth G], M [auth A], N [auth A], OA [auth H], PA [auth H], R [auth B], SA [auth I], TA [auth J], U [auth C], VA [auth K], X [auth D], XA [auth L], Y [auth D], YA [auth L]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain R [auth B] Focus chain SA [auth I] Focus chain TA [auth J] Focus chain U [auth C] Focus chain VA [auth K] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain YA [auth L] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain R [auth B] Focus chain SA [auth I] Focus chain TA [auth J] Focus chain U [auth C] Focus chain VA [auth K] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain YA [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain BA [auth D] SDF format, chain IA [auth F] SDF format, chain NA [auth G] SDF format, chain Q [auth A] SDF format, chain RA [auth H] MOL2 format, chain AB [auth L] MOL2 format, chain BA [auth D] MOL2 format, chain IA [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth H] mmCIF format, chain AB [auth L] mmCIF format, chain BA [auth D] mmCIF format, chain IA [auth F] mmCIF format, chain NA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth H]	AB [auth L] BA [auth D] IA [auth F] NA [auth G] Q [auth A] AB [auth L], BA [auth D], IA [auth F], NA [auth G], Q [auth A], RA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth L] Focus chain BA [auth D] Focus chain IA [auth F] Focus chain NA [auth G] Focus chain Q [auth A] Focus chain RA [auth H] Interactions & Density Focus chain AB [auth L] Focus chain BA [auth D] Focus chain IA [auth F] Focus chain NA [auth G] Focus chain Q [auth A] Focus chain RA [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth E] SDF format, chain HA [auth F] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth H] SDF format, chain S [auth B] SDF format, chain UA [auth J] SDF format, chain V [auth C] SDF format, chain WA [auth K] SDF format, chain Z [auth D] SDF format, chain ZA [auth L] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth J] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth K] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth L] mmCIF format, chain AA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth J] mmCIF format, chain V [auth C] mmCIF format, chain WA [auth K] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth L]	AA [auth D] DA [auth E] HA [auth F] LA [auth G] MA [auth G] AA [auth D], DA [auth E], HA [auth F], LA [auth G], MA [auth G], O [auth A], P [auth A], QA [auth H], S [auth B], UA [auth J], V [auth C], WA [auth K], Z [auth D], ZA [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth H] Focus chain S [auth B] Focus chain UA [auth J] Focus chain V [auth C] Focus chain WA [auth K] Focus chain Z [auth D] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth H] Focus chain S [auth B] Focus chain UA [auth J] Focus chain V [auth C] Focus chain WA [auth K] Focus chain Z [auth D] Focus chain ZA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.176
R-Value Work: 0.147
R-Value Observed: 0.148
Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.62	α = 90
b = 126.62	β = 90
c = 174.86	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Kuenzle, M.

Beck, T.

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description