6H6T | pdb_00006h6t

Binary crystal structure of positively and negatively supercharged variants Ftn(pos) and Ftn(neg) from human heavy chain ferritin (propandiol condition, coordination number 8)

PDB DOI: https://doi.org/10.2210/pdb6H6T/pdb

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

Deposited: 2018-07-30 Released: 2019-08-14
Deposition Author(s): Kuenzle, M., Lach, M., Beck, T.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.222 (Depositor), 0.230 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Self-assembly of protein crystals into different crystal structures using charged patches on oppositely charged ferritin protein containers

Kuenzle, M., Lach, M., Beck, T.

To be published.

Macromolecule Content

Total Structure Weight: 258.57 kDa
Atom Count: 17,707
Modeled Residue Count: 2,067
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain JA [auth K] SDF format, chain V [auth E] SDF format, chain Y [auth F] SDF format, chain R [auth C] SDF format, chain LA [auth L] SDF format, chain GA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain R [auth C] MOL2 format, chain LA [auth L] MOL2 format, chain GA [auth J] mmCIF format, chain JA [auth K] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain R [auth C] mmCIF format, chain LA [auth L] mmCIF format, chain GA [auth J]	GA [auth J] JA [auth K] LA [auth L] R [auth C] V [auth E] GA [auth J], JA [auth K], LA [auth L], R [auth C], V [auth E], Y [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain R [auth C] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain GA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain R [auth C] Focus chain V [auth E] Focus chain Y [auth F]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain CA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain CA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain CA [auth G]	CA [auth G], N [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth G] Focus chain N [auth A] Interactions & Density Focus chain CA [auth G] Focus chain N [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain HA [auth J] SDF format, chain KA [auth K] SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain MA [auth L] SDF format, chain M [auth A] SDF format, chain FA [auth I] SDF format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain HA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain MA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain FA [auth I] MOL2 format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain HA [auth J] mmCIF format, chain KA [auth K] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain MA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain FA [auth I] mmCIF format, chain BA [auth G]	BA [auth G] EA [auth H] FA [auth I] HA [auth J] KA [auth K] BA [auth G], EA [auth H], FA [auth I], HA [auth J], KA [auth K], M [auth A], MA [auth L], P [auth B], S [auth C], U [auth D], W [auth E], Z [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain M [auth A] Focus chain MA [auth L] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain M [auth A] Focus chain MA [auth L] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Z [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain IA [auth J] SDF format, chain X [auth E] SDF format, chain T [auth C] SDF format, chain NA [auth L] SDF format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain IA [auth J] MOL2 format, chain X [auth E] MOL2 format, chain T [auth C] MOL2 format, chain NA [auth L] MOL2 format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain IA [auth J] mmCIF format, chain X [auth E] mmCIF format, chain T [auth C] mmCIF format, chain NA [auth L] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] IA [auth J] NA [auth L] T [auth C] AA [auth F], DA [auth G], IA [auth J], NA [auth L], T [auth C], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain IA [auth J] Focus chain NA [auth L] Focus chain T [auth C] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain IA [auth J] Focus chain NA [auth L] Focus chain T [auth C] Focus chain X [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth A]	O [auth A], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Q [auth B] Interactions & Density Focus chain O [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222 (Depositor), 0.230 (DCC)
R-Value Work: 0.182 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.229	α = 90
b = 153.229	β = 90
c = 135.803	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Kuenzle, M.

Lach, M.

Beck, T.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description