3BKN

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
R-Value Work: 0.179
R-Value Observed: 0.181

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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1110/ps.034819.108
Primary Citation of 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
Modelled Residue Count: 1,932
Deposited Residue Count: 1,932
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, 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 FA [auth E] SDF format, chain OA [auth H] SDF format, chain EB [auth L] 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 FA [auth E] MOL2 format, chain OA [auth H] MOL2 format, chain EB [auth L] 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 FA [auth E] mmCIF format, chain OA [auth H] mmCIF format, chain EB [auth L] 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]
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]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth E] SDF format, chain DB [auth L] SDF format, chain LA [auth H] SDF format, chain P [auth B] SDF format, chain PA [auth I] SDF format, chain Q [auth B] SDF format, chain UA [auth J] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain CA [auth E] SDF format, chain CB [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 M [auth A] SDF format, chain MA [auth H] SDF format, chain N [auth A] SDF format, chain QA [auth I] SDF format, chain VA [auth J] SDF format, chain YA [auth K] SDF format, chain Z [auth D] SDF format, chain ZA [auth K] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth L] MOL2 format, chain LA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain UA [auth J] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain CB [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 M [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth I] MOL2 format, chain VA [auth J] MOL2 format, chain YA [auth K] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth K] mmCIF format, chain AA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain DB [auth L] mmCIF format, chain LA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain UA [auth J] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain CB [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 M [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth I] mmCIF format, chain VA [auth J] mmCIF format, chain YA [auth K] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth K]	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]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BB [auth L] SDF format, chain EA [auth E] SDF format, chain NA [auth H] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain XA [auth K] SDF format, chain IA [auth F] SDF format, chain O [auth A] SDF format, chain RA [auth I] SDF format, chain TA [auth J] SDF format, chain X [auth C] MOL2 format, chain BB [auth L] MOL2 format, chain EA [auth E] MOL2 format, chain NA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain XA [auth K] MOL2 format, chain IA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain RA [auth I] MOL2 format, chain TA [auth J] MOL2 format, chain X [auth C] mmCIF format, chain BB [auth L] mmCIF format, chain EA [auth E] mmCIF format, chain NA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain XA [auth K] mmCIF format, chain IA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain RA [auth I] mmCIF format, chain TA [auth J] mmCIF format, chain X [auth C]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.228
R-Value Work: 0.179
R-Value Observed: 0.181
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

View Full Validation Report

Ligand Structure Quality Assessment

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