1BFR

IRON STORAGE AND ELECTRON TRANSPORT

PDB DOI: https://doi.org/10.2210/pdb1BFR/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 1994-12-16 Released: 1996-06-20
Deposition Author(s): Dautant, A., Yariv, J., Meyer, J.B., Precigoux, G., Sweet, R.M., Frolow, F., Kalb(Gilboa), A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Work: 0.216
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

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

Literature

Structure of a monoclinic crystal from of cyctochrome b1 (Bacterioferritin) from E. coli.

Dautant, A., Meyer, J.B., Yariv, J., Precigoux, G., Sweet, R.M., Kalb, A.J., Frolow, F.

(1998) Acta Crystallogr D Biol Crystallogr 54: 16-24

PubMed: 9867433 Search on PubMed
DOI: https://doi.org/10.1107/s0907444997006811
Primary Citation of Related Structures:
1BFR

PubMed Abstract:
Crystals of E. coli cytochrome b1, alias bacterioferritin, were grown fr om a low ionic strength solution. The resulting monoclniic P21 structure was solved by molecular replacement and refined using noncrystallographi c symmetries applied to the fundamental unit, consisting of two protein subunits and a single haem. From the Patterson self-rotation results it was shown that the asymmetric unit of the monoclinic crystal consists of 12 such dimers and corresponds to a complete, nearly spherical, molecule of bacterioferritin (M4 = 450 kDa) of 432 point-group symmetry. It is thus the most symmetrical cytochrome. As previously determined for the tetragonal form, the haem is located in a special position on a local twofold axis of the dimer. A bimetal centre is also observed within the four-helix bundle of each monomer; a metal-binding site is located on the fourfold axis.

Organizational Affiliation

Unité Biophysique Structurale, ERS133 CNRS, Université de Bordeaux 1, France.

Macromolecule Content

Total Structure Weight: 454.47 kDa
Atom Count: 31,740
Modelled Residue Count: 3,792
Deposited Residue Count: 3,792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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, M, N, O, P, Q, R, S, T, U, V, W, X	158	Escherichia coli	Mutation(s): 0
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

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 AC [auth V] SDF format, chain BB [auth L] SDF format, chain CA [auth B] SDF format, chain FC [auth X] SDF format, chain GB [auth N] SDF format, chain HA [auth D] SDF format, chain LB [auth P] SDF format, chain MA [auth F] SDF format, chain QB [auth R] SDF format, chain RA [auth H] SDF format, chain VB [auth T] SDF format, chain WA [auth J] MOL2 format, chain AC [auth V] MOL2 format, chain BB [auth L] MOL2 format, chain CA [auth B] MOL2 format, chain FC [auth X] MOL2 format, chain GB [auth N] MOL2 format, chain HA [auth D] MOL2 format, chain LB [auth P] MOL2 format, chain MA [auth F] MOL2 format, chain QB [auth R] MOL2 format, chain RA [auth H] MOL2 format, chain VB [auth T] MOL2 format, chain WA [auth J]	AC [auth V] BB [auth L] CA [auth B] FC [auth X] GB [auth N] AC [auth V], BB [auth L], CA [auth B], FC [auth X], GB [auth N], HA [auth D], LB [auth P], MA [auth F], QB [auth R], RA [auth H], VB [auth T], WA [auth J]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AC [auth V] Focus chain BB [auth L] Focus chain CA [auth B] Focus chain FC [auth X] Focus chain GB [auth N] Focus chain HA [auth D] Focus chain LB [auth P] Focus chain MA [auth F] Focus chain QB [auth R] Focus chain RA [auth H] Focus chain VB [auth T] Focus chain WA [auth J]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth L] SDF format, chain BA [auth B] SDF format, chain BC [auth W] SDF format, chain CB [auth M] SDF format, chain CC [auth W] SDF format, chain DA [auth C] SDF format, chain DB [auth M] SDF format, chain DC [auth X] SDF format, chain EA [auth C] SDF format, chain EB [auth N] SDF format, chain EC [auth X] SDF format, chain FA [auth D] SDF format, chain FB [auth N] SDF format, chain GA [auth D] SDF format, chain HB [auth O] SDF format, chain IA [auth E] SDF format, chain IB [auth O] SDF format, chain JA [auth E] SDF format, chain JB [auth P] SDF format, chain KA [auth F] SDF format, chain KB [auth P] SDF format, chain LA [auth F] SDF format, chain MB [auth Q] SDF format, chain NA [auth G] SDF format, chain NB [auth Q] SDF format, chain OA [auth G] SDF format, chain OB [auth R] SDF format, chain PA [auth H] SDF format, chain PB [auth R] SDF format, chain QA [auth H] SDF format, chain RB [auth S] SDF format, chain SA [auth I] SDF format, chain SB [auth S] SDF format, chain TA [auth I] SDF format, chain TB [auth T] SDF format, chain UA [auth J] SDF format, chain UB [auth T] SDF format, chain VA [auth J] SDF format, chain WB [auth U] SDF format, chain XA [auth K] SDF format, chain XB [auth U] SDF format, chain Y [auth A] SDF format, chain YA [auth K] SDF format, chain YB [auth V] SDF format, chain Z [auth A] SDF format, chain ZA [auth L] SDF format, chain ZB [auth V] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth L] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth W] MOL2 format, chain CB [auth M] MOL2 format, chain CC [auth W] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth M] MOL2 format, chain DC [auth X] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth N] MOL2 format, chain EC [auth X] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth N] MOL2 format, chain GA [auth D] MOL2 format, chain HB [auth O] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth O] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth P] MOL2 format, chain KA [auth F] MOL2 format, chain KB [auth P] MOL2 format, chain LA [auth F] MOL2 format, chain MB [auth Q] MOL2 format, chain NA [auth G] MOL2 format, chain NB [auth Q] MOL2 format, chain OA [auth G] MOL2 format, chain OB [auth R] MOL2 format, chain PA [auth H] MOL2 format, chain PB [auth R] MOL2 format, chain QA [auth H] MOL2 format, chain RB [auth S] MOL2 format, chain SA [auth I] MOL2 format, chain SB [auth S] MOL2 format, chain TA [auth I] MOL2 format, chain TB [auth T] MOL2 format, chain UA [auth J] MOL2 format, chain UB [auth T] MOL2 format, chain VA [auth J] MOL2 format, chain WB [auth U] MOL2 format, chain XA [auth K] MOL2 format, chain XB [auth U] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth K] MOL2 format, chain YB [auth V] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth L] MOL2 format, chain ZB [auth V]	AA [auth B] AB [auth L] BA [auth B] BC [auth W] CB [auth M] AA [auth B], AB [auth L], BA [auth B], BC [auth W], CB [auth M], CC [auth W], DA [auth C], DB [auth M], DC [auth X], EA [auth C], EB [auth N], EC [auth X], FA [auth D], FB [auth N], GA [auth D], HB [auth O], IA [auth E], IB [auth O], JA [auth E], JB [auth P], KA [auth F], KB [auth P], LA [auth F], MB [auth Q], NA [auth G], NB [auth Q], OA [auth G], OB [auth R], PA [auth H], PB [auth R], QA [auth H], RB [auth S], SA [auth I], SB [auth S], TA [auth I], TB [auth T], UA [auth J], UB [auth T], VA [auth J], WB [auth U], XA [auth K], XB [auth U], Y [auth A], YA [auth K], YB [auth V], Z [auth A], ZA [auth L], ZB [auth V]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth L] Focus chain BA [auth B] Focus chain BC [auth W] Focus chain CB [auth M] Focus chain CC [auth W] Focus chain DA [auth C] Focus chain DB [auth M] Focus chain DC [auth X] Focus chain EA [auth C] Focus chain EB [auth N] Focus chain EC [auth X] Focus chain FA [auth D] Focus chain FB [auth N] Focus chain GA [auth D] Focus chain HB [auth O] Focus chain IA [auth E] Focus chain IB [auth O] Focus chain JA [auth E] Focus chain JB [auth P] Focus chain KA [auth F] Focus chain KB [auth P] Focus chain LA [auth F] Focus chain MB [auth Q] Focus chain NA [auth G] Focus chain NB [auth Q] Focus chain OA [auth G] Focus chain OB [auth R] Focus chain PA [auth H] Focus chain PB [auth R] Focus chain QA [auth H] Focus chain RB [auth S] Focus chain SA [auth I] Focus chain SB [auth S] Focus chain TA [auth I] Focus chain TB [auth T] Focus chain UA [auth J] Focus chain UB [auth T] Focus chain VA [auth J] Focus chain WB [auth U] Focus chain XA [auth K] Focus chain XB [auth U] Focus chain Y [auth A] Focus chain YA [auth K] Focus chain YB [auth V] Focus chain Z [auth A] Focus chain ZA [auth L] Focus chain ZB [auth V]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Work: 0.216
R-Value Observed: 0.216
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.7	α = 90
b = 211.6	β = 119.1
c = 123.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1996-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1996-06-20
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Other