5HJH

Dps4 from Nostoc punctiforme in complex with Fe ions

PDB DOI: https://doi.org/10.2210/pdb5HJH/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Nostoc punctiforme
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-01-13 Released: 2017-01-25
Deposition Author(s): Howe, C., Moparthi, V.K., Persson, K., Stensjo, K.
Funding Organization(s): Swedish Energy Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.193 (Depositor)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Dps4 from Nostoc punctiforme in complex with Fe ions

Howe, C., Moparthi, V.K., Persson, K., Stensjo, K.

To be published.

Macromolecule Content

Total Structure Weight: 81.25 kDa
Atom Count: 6,063
Modelled Residue Count: 709
Deposited Residue Count: 712
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, Dps family protein	A, B, C, D	178	Nostoc punctiforme	Mutation(s): 0 Gene Names: Npun_R5799
UniProt
Find proteins for B2J981 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J981 Go to UniProtKB: B2J981
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2J981
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	E [auth A] G [auth A] H [auth A] I [auth B] J [auth C] E [auth A], G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.193 (Depositor)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.31	α = 90
b = 100.31	β = 90
c = 145.65	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Energy Agency	Sweden	11674-5

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description