2HTN | pdb_00002htn

E. coli bacterioferritin in its as-isolated form

PDB DOI: https://doi.org/10.2210/pdb2HTN/pdb

Classification: METAL BINDING PROTEIN, OXIDOREDUCTASE
Organism(s): Escherichia coli BL21
Mutation(s): No

Deposited: 2006-07-26 Released: 2006-11-21
Deposition Author(s): van Eerde, A., Wolterink-Van Loo, S., Van Der Oost, J., Dijkstra, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.188 (Depositor)
R-Value Work:
0.171 (Depositor), 0.160 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form.

van Eerde, A., Wolterink-van Loo, S., van der Oost, J., Dijkstra, B.W.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1061-1066

PubMed: 17077480 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309106039583
Primary Citation of Related Structures:
2HTN

PubMed Abstract:
Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 A resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on 'as-isolated' E. coli bacterioferritin. The ferroxidase active site contains positive difference density consistent with two metal ions that had co-purified with the protein. X-ray fluorescence studies suggest that the metal composition is different from that of previous structures and is a mix of zinc and native iron ions. The ferroxidase-centre configuration displays a similar flexibility as previously noted for other bacterioferritins.

Organizational Affiliation

Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 151.5 kDa
Atom Count: 10,846
Modelled Residue Count: 1,264
Deposited Residue Count: 1,264
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A, B, C, D, E A, B, C, D, E, F, G, H	158	Escherichia coli BL21	Mutation(s): 0 EC: 1.16.3.1
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12)) Explore P0ABD3 Go to UniProtKB: P0ABD3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABD3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth C] SDF format, chain U [auth E] SDF format, chain Z [auth G] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Z [auth G] mmCIF format, chain K [auth A] mmCIF format, chain P [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Z [auth G]	K [auth A], P [auth C], U [auth E], Z [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain K [auth A] Focus chain P [auth C] Focus chain U [auth E] Focus chain Z [auth G] Interactions & Density Focus chain K [auth A] Focus chain P [auth C] Focus chain U [auth E] Focus chain Z [auth G]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain I [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain AA [auth H] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain X [auth G] SDF format, chain Y [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain AA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain AA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G]	AA [auth H] BA [auth H] I [auth A] J [auth A] L [auth B] AA [auth H], BA [auth H], I [auth A], J [auth A], L [auth B], M [auth B], N [auth C], O [auth C], Q [auth D], R [auth D], S [auth E], T [auth E], V [auth F], W [auth F], X [auth G], Y [auth G]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.188 (Depositor)
R-Value Work: 0.171 (Depositor), 0.160 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.893	α = 90
b = 167.893	β = 90
c = 167.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-11-21

Deposition Author(s):

van Eerde, A.

Wolterink-Van Loo, S.

Van Der Oost, J.

Dijkstra, B.W.

Revision History (Full details and data files)

Version 1.0: 2006-11-21
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2014-11-12
Changes: Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

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E. coli bacterioferritin in its as-isolated form

Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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