3WNW | pdb_00003wnw

Structure of Mouse H-chain modified ferritin

PDB DOI: https://doi.org/10.2210/pdb3WNW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-17 Released: 2015-01-28
Deposition Author(s): Zarivach, R., Lewin, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.220 (Depositor), 0.230 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6SHT

Literature

Studies of ferritin-M6A

Zarivach, R., Lewin, L.

To be published.

Macromolecule Content

Total Structure Weight: 291.7 kDa
Atom Count: 18,648
Modeled Residue Count: 2,080
Deposited Residue Count: 2,544
Unique protein chains: 1

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, G, H, I, J, K, L	212	Mus musculus	Mutation(s): 0 Gene Names: Fth1, Fth EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P09528 (Mus musculus) Explore P09528 Go to UniProtKB: P09528
IMPC: MGI:95588
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09528
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 CA [auth D] SDF format, chain DA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain TA [auth K] SDF format, chain UA [auth K] SDF format, chain WA [auth L] SDF format, chain X [auth C] SDF format, chain XA [auth L] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth K] MOL2 format, chain UA [auth K] MOL2 format, chain WA [auth L] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth L] MOL2 format, chain Y [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain TA [auth K] mmCIF format, chain UA [auth K] mmCIF format, chain WA [auth L] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth L] mmCIF format, chain Y [auth C]	CA [auth D] DA [auth D] GA [auth E] HA [auth E] P [auth A] CA [auth D], DA [auth D], GA [auth E], HA [auth E], P [auth A], Q [auth A], TA [auth K], UA [auth K], WA [auth L], X [auth C], XA [auth L], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth K] Focus chain UA [auth K] Focus chain WA [auth L] Focus chain X [auth C] Focus chain XA [auth L] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth K] Focus chain UA [auth K] Focus chain WA [auth L] Focus chain X [auth C] Focus chain XA [auth L] Focus chain Y [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain MA [auth H] SDF format, chain O [auth A] SDF format, chain S [auth B] SDF format, chain W [auth C] MOL2 format, chain MA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] mmCIF format, chain MA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C]	MA [auth H], O [auth A], S [auth B], W [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain MA [auth H] Focus chain O [auth A] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain MA [auth H] Focus chain O [auth A] Focus chain S [auth B] Focus chain W [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	T [auth B], Z [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain T [auth B] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain IA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain LA [auth H] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth I] SDF format, chain OA [auth I] SDF format, chain PA [auth J] SDF format, chain QA [auth J] SDF format, chain R [auth B] SDF format, chain RA [auth K] SDF format, chain SA [auth K] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain VA [auth L] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth K] MOL2 format, chain SA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth L] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain OA [auth I] mmCIF format, chain PA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth K] mmCIF format, chain SA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth L]	AA [auth D] BA [auth D] EA [auth E] FA [auth E] IA [auth F] AA [auth D], BA [auth D], EA [auth E], FA [auth E], IA [auth F], JA [auth G], KA [auth G], LA [auth H], M [auth A], N [auth A], NA [auth I], OA [auth I], PA [auth J], QA [auth J], R [auth B], RA [auth K], SA [auth K], U [auth C], V [auth C], VA [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth L] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.265 (Depositor), 0.270 (DCC)
R-Value Work: 0.220 (Depositor), 0.230 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.145	α = 90
b = 218.145	β = 90
c = 147.69	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Zarivach, R.

Lewin, L.

Revision History (Full details and data files)

Version 1.0: 2015-01-28
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description