3SH6 | pdb_00003sh6

Frog M-ferritin, D122R mutant, with magnesium

PDB DOI: https://doi.org/10.2210/pdb3SH6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aquarana catesbeiana
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-06-16 Released: 2012-02-29
Deposition Author(s): Tosha, T., Ng, H.L., Alber, T., Theil, E.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.192 (Depositor), 0.194 (DCC)
R-Value Work:
0.166 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3SH6

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

Literature

Frog M-ferritin, D122R mutant, with magnesium

Tosha, T., Ng, H.L., Alber, T., Theil, E.C.

To be published.

Macromolecule Content

Total Structure Weight: 20.94 kDa
Atom Count: 1,700
Modeled Residue Count: 174
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin, middle subunit	A	176	Aquarana catesbeiana	Mutation(s): 1 EC: 1.16.3.1
UniProt
Find proteins for P07798 (Aquarana catesbeiana) Explore P07798 Go to UniProtKB: P07798
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07798
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain C [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.192 (Depositor), 0.194 (DCC)
R-Value Work: 0.166 (Depositor), 0.167 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.374	α = 90
b = 183.374	β = 90
c = 183.374	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.