1SOF | pdb_00001sof

Crystal structure of the azotobacter vinelandii bacterioferritin at 2.6 A resolution

PDB DOI: https://doi.org/10.2210/pdb1SOF/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Azotobacter vinelandii
Mutation(s): No

Deposited: 2004-03-14 Released: 2005-04-05
Deposition Author(s): Liu, H.L., Huang, J.F., Bi, R.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.246 (Depositor), 0.233 (DCC)
R-Value Work:
0.196 (Depositor), 0.187 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

2.6 A resolution crystal structure of the bacterioferritin from Azotobacter vinelandii

Liu, H.L., Zhou, H.N., Xing, W.M., Zhao, J.F., Li, S.X., Huang, J.F., Bi, R.C.

(2004) FEBS Lett 573: 93-98

PubMed: 15327981 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2004.07.054
Primary Citation Related Structures:
1SOF

PubMed Abstract:
The crystal structure of the bacterioferritin from Azotobacter vinelandii has been determined at 2.6 A resolution. Both the low occupancy of one iron ion in the dinuclear iron center and the deviation of its adjacent residue His130 from the center suggest migration of the iron ion from the dinuclear iron site to the inner nucleation site. The concerted movement of His130 and Glu47 may admit a dynamic gating mechanism for shift of the oxidized iron ion. Ba2+ binding to the fourfold channel implicates that the channel bears Fe2+ conductivity and selectivity to provide a route for iron access to the inner cavity during core formation.

Organizational Affiliation

Institute of Biophysics, Chinese Academy of Sciences, Datun Road 15, Chaoyang District, Beijing 100101, China.

Macromolecule Content

Total Structure Weight: 148.9 kDa
Atom Count: 10,498
Modeled Residue Count: 1,240
Deposited Residue Count: 1,248
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	156	Azotobacter vinelandii	Mutation(s): 0 EC: 1.16.3.1
UniProt
Find proteins for P22759 (Azotobacter vinelandii) Explore P22759 Go to UniProtKB: P22759
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22759
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 CA [auth E] SDF format, chain KA [auth G] SDF format, chain P [auth B] SDF format, chain T [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain KA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain KA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C]	CA [auth E], KA [auth G], P [auth B], T [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CA [auth E] Focus chain KA [auth G] Focus chain P [auth B] Focus chain T [auth C] Interactions & Density Focus chain CA [auth E] Focus chain KA [auth G] Focus chain P [auth B] Focus chain T [auth C]
BA Query on BA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Z [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Z [auth D]	L [auth A], Z [auth D]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Z [auth D] Interactions & Density Focus chain L [auth A] Focus chain Z [auth D]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth G] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] HA [auth G] AA [auth E], BA [auth E], DA [auth F], EA [auth F], HA [auth G], I [auth A], IA [auth G], J [auth A], LA [auth H], M [auth B], MA [auth H], N [auth B], Q [auth C], R [auth C], U [auth D], V [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain LA [auth H] Focus chain M [auth B] Focus chain MA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain LA [auth H] Focus chain M [auth B] Focus chain MA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain JA [auth G] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain NA [auth H] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain NA [auth H] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain NA [auth H]	FA [auth F] GA [auth F] JA [auth G] K [auth A] NA [auth H] FA [auth F], GA [auth F], JA [auth G], K [auth A], NA [auth H], O [auth B], S [auth C], W [auth D], X [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth F] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain K [auth A] Focus chain NA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain FA [auth F] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain K [auth A] Focus chain NA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.246 (Depositor), 0.233 (DCC)
R-Value Work: 0.196 (Depositor), 0.187 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.965	α = 90
b = 124.965	β = 90
c = 287.406	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Liu, H.L.

Huang, J.F.

Bi, R.C.

Revision History (Full details and data files)

Version 1.0: 2005-04-05
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description