3BKN | pdb_00003bkn

The structure of Mycobacterial bacterioferritin

PDB DOI: https://doi.org/10.2210/pdb3BKN/pdb
Entry: 3BKN supersedes: 3B3H

Classification: METAL BINDING PROTEIN
Organism(s): Mycolicibacterium smegmatis MC2 155
Mutation(s): No

Deposited: 2007-12-07 Released: 2008-01-22
Deposition Author(s): Janowski, R., Auerbach-Nevo, T., Weiss, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.228 (Depositor), 0.233 (DCC)
R-Value Work:
0.179 (Depositor), 0.186 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site.

Janowski, R., Auerbach-Nevo, T., Weiss, M.S.

(2008) Protein Sci 17: 1138-1150

PubMed: 18445621 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1110/ps.034819.108
Primary Citation Related Structures:
3BKN

PubMed Abstract:
Bacterioferritins, also known as cytochrome b (1), are oligomeric iron-storage proteins consisting of 24 identical amino acid chains, which form spherical particles consisting of 24 subunits and exhibiting 432 point-group symmetry. They contain one haem b molecule at the interface between two subunits and a di-nuclear metal binding center. The X-ray structure of bacterioferritin from Mycobacterium smegmatis (Ms-Bfr) was determined to a resolution of 2.7 A in the monoclinic space group C2. The asymmetric unit of the crystals contains 12 protein molecules: five dimers and two half-dimers located along the crystallographic twofold axis. Unexpectedly, the di-nuclear metal binding center contains zinc ions instead of the typically observed iron ions in other bacterioferritins.

Organizational Affiliation

EMBL Hamburg Outstation, D-22603 Hamburg, Germany.

Macromolecule Content

Total Structure Weight: 228.66 kDa
Atom Count: 16,205
Modeled Residue Count: 1,932
Deposited Residue Count: 1,932
Unique protein chains: 1

Macromolecules

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| 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, I, J, K, L	161	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 1.16.3.1
UniProt
Find proteins for A0QY79 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QY79 Go to UniProtKB: A0QY79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QY79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain EB [auth L] SDF format, chain FA [auth E] SDF format, chain OA [auth H] SDF format, chain SA [auth I] SDF format, chain T [auth B] SDF format, chain Y [auth C] MOL2 format, chain AB [auth K] MOL2 format, chain EB [auth L] MOL2 format, chain FA [auth E] MOL2 format, chain OA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain AB [auth K] mmCIF format, chain EB [auth L] mmCIF format, chain FA [auth E] mmCIF format, chain OA [auth H] mmCIF format, chain SA [auth I] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C]	AB [auth K] EB [auth L] FA [auth E] OA [auth H] SA [auth I] AB [auth K], EB [auth L], FA [auth E], OA [auth H], SA [auth I], T [auth B], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AB [auth K] Focus chain EB [auth L] Focus chain FA [auth E] Focus chain OA [auth H] Focus chain SA [auth I] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AB [auth K] Focus chain EB [auth L] Focus chain FA [auth E] Focus chain OA [auth H] Focus chain SA [auth I] Focus chain T [auth B] Focus chain Y [auth C]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain WA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain WA [auth J] mmCIF format, chain BA [auth D] mmCIF format, chain WA [auth J]	BA [auth D], WA [auth J]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain WA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain WA [auth J]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain DB [auth L] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain PA [auth I] SDF format, chain Q [auth B] SDF format, chain QA [auth I] SDF format, chain UA [auth J] SDF format, chain V [auth C] SDF format, chain VA [auth J] SDF format, chain W [auth C] SDF format, chain YA [auth K] SDF format, chain Z [auth D] SDF format, chain ZA [auth K] SDF format, chain M [auth A] SDF format, chain CB [auth L] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain UA [auth J] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth J] MOL2 format, chain W [auth C] MOL2 format, chain YA [auth K] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain CB [auth L] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain DB [auth L] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth I] mmCIF format, chain UA [auth J] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth J] mmCIF format, chain W [auth C] mmCIF format, chain YA [auth K] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain CB [auth L]	AA [auth D] CA [auth E] CB [auth L] DA [auth E] DB [auth L] AA [auth D], CA [auth E], CB [auth L], DA [auth E], DB [auth L], GA [auth F], HA [auth F], JA [auth G], KA [auth G], LA [auth H], M [auth A], MA [auth H], N [auth A], P [auth B], PA [auth I], Q [auth B], QA [auth I], UA [auth J], V [auth C], VA [auth J], W [auth C], YA [auth K], Z [auth D], ZA [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain CB [auth L] Focus chain DA [auth E] Focus chain DB [auth L] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain UA [auth J] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth C] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain CB [auth L] Focus chain DA [auth E] Focus chain DB [auth L] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain UA [auth J] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth C] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BB [auth L] SDF format, chain EA [auth E] SDF format, chain IA [auth F] SDF format, chain NA [auth H] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain RA [auth I] SDF format, chain S [auth B] SDF format, chain TA [auth J] SDF format, chain U [auth C] SDF format, chain X [auth C] SDF format, chain XA [auth K] MOL2 format, chain BB [auth L] MOL2 format, chain EA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth K] mmCIF format, chain BB [auth L] mmCIF format, chain EA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain NA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth J] mmCIF format, chain U [auth C] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth K]	BB [auth L] EA [auth E] IA [auth F] NA [auth H] O [auth A] BB [auth L], EA [auth E], IA [auth F], NA [auth H], O [auth A], R [auth B], RA [auth I], S [auth B], TA [auth J], U [auth C], X [auth C], XA [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth L] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain NA [auth H] Focus chain O [auth A] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain TA [auth J] Focus chain U [auth C] Focus chain X [auth C] Focus chain XA [auth K] Interactions & Density Focus chain BB [auth L] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain NA [auth H] Focus chain O [auth A] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain TA [auth J] Focus chain U [auth C] Focus chain X [auth C] Focus chain XA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.228 (Depositor), 0.233 (DCC)
R-Value Work: 0.179 (Depositor), 0.186 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.523	α = 90
b = 151.52	β = 128.08
c = 116.715	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-01-22

Deposition Author(s):

Janowski, R.

Auerbach-Nevo, T.

Weiss, M.S.

This entry supersedes: 3B3H

Revision History (Full details and data files)

Version 1.0: 2008-01-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description