2VXI | pdb_00002vxi

The binding of heme and zinc in Escherichia coli Bacterioferritin

PDB DOI: https://doi.org/10.2210/pdb2VXI/pdb

Classification: METAL TRANSPORT
Organism(s): Escherichia coli BL21
Mutation(s): No

Deposited: 2008-07-04 Released: 2008-11-04
Deposition Author(s): Willies, S.C., Isupov, M.N., Garman, E.F., Littlechild, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Binding of Haem and Zinc in the 1.9 A X-Ray Structure of Escherichia Coli Bacterioferritin.

Willies, S.C., Isupov, M.N., Garman, E.F., Littlechild, J.A.

(2009) J Biol Inorg Chem 14: 201

PubMed: 18946693 Search on PubMed
DOI: https://doi.org/10.1007/s00775-008-0438-8
Primary Citation Related Structures:
2VXI

PubMed Abstract:
The crystal structure of Escherichia coli bacterioferritin has been solved to 1.9 A, and shows the symmetrical binding of a haem molecule on the local twofold axis between subunits and a pair of metal atoms bound to each subunit at the ferroxidase centre. These metals have been identified as zinc by the analysis of the structure and X-ray data and confirmed by microfocused proton-induced X-ray emission experiments. For the first time the haem has been shown to be linked to both the internal and the external environments via a cluster of waters positioned above the haem molecule.

Organizational Affiliation

School of Biosciences, Henry Wellcome Building for Biocatalysis, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.

Macromolecule Content

Total Structure Weight: 233.97 kDa
Atom Count: 18,818
Modeled Residue Count: 1,884
Deposited Residue Count: 1,896
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	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain Z [auth C] SDF format, chain UB [auth L] SDF format, chain UA [auth G] SDF format, chain S [auth B] SDF format, chain QA [auth F] SDF format, chain PB [auth K] SDF format, chain M [auth A] SDF format, chain KB [auth J] SDF format, chain KA [auth E] SDF format, chain FB [auth I] SDF format, chain FA [auth D] MOL2 format, chain ZA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain UB [auth L] MOL2 format, chain UA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain PB [auth K] MOL2 format, chain M [auth A] MOL2 format, chain KB [auth J] MOL2 format, chain KA [auth E] MOL2 format, chain FB [auth I] MOL2 format, chain FA [auth D] mmCIF format, chain ZA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain UB [auth L] mmCIF format, chain UA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain PB [auth K] mmCIF format, chain M [auth A] mmCIF format, chain KB [auth J] mmCIF format, chain KA [auth E] mmCIF format, chain FB [auth I] mmCIF format, chain FA [auth D]	FA [auth D] FB [auth I] KA [auth E] KB [auth J] M [auth A] FA [auth D], FB [auth I], KA [auth E], KB [auth J], M [auth A], PB [auth K], QA [auth F], S [auth B], UA [auth G], UB [auth L], Z [auth C], ZA [auth H]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain FA [auth D] Focus chain FB [auth I] Focus chain KA [auth E] Focus chain KB [auth J] Focus chain M [auth A] Focus chain PB [auth K] Focus chain QA [auth F] Focus chain S [auth B] Focus chain UA [auth G] Focus chain UB [auth L] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain FA [auth D] Focus chain FB [auth I] Focus chain KA [auth E] Focus chain KB [auth J] Focus chain M [auth A] Focus chain PB [auth K] Focus chain QA [auth F] Focus chain S [auth B] Focus chain UA [auth G] Focus chain UB [auth L] Focus chain Z [auth C] Focus chain ZA [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain YB [auth L] SDF format, chain YA [auth G] SDF format, chain Y [auth B] SDF format, chain XB [auth L] SDF format, chain XA [auth G] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain TB [auth K] SDF format, chain TA [auth F] SDF format, chain SB [auth K] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain PA [auth E] SDF format, chain P [auth A] SDF format, chain OB [auth J] SDF format, chain OA [auth E] SDF format, chain NB [auth J] SDF format, chain NA [auth E] SDF format, chain JB [auth I] SDF format, chain JA [auth D] SDF format, chain IB [auth I] SDF format, chain IA [auth D] SDF format, chain EB [auth H] SDF format, chain EA [auth C] SDF format, chain DB [auth H] SDF format, chain DA [auth C] SDF format, chain CB [auth H] SDF format, chain CA [auth C] MOL2 format, chain YB [auth L] MOL2 format, chain YA [auth G] MOL2 format, chain Y [auth B] MOL2 format, chain XB [auth L] MOL2 format, chain XA [auth G] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain TB [auth K] MOL2 format, chain TA [auth F] MOL2 format, chain SB [auth K] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth J] MOL2 format, chain OA [auth E] MOL2 format, chain NB [auth J] MOL2 format, chain NA [auth E] MOL2 format, chain JB [auth I] MOL2 format, chain JA [auth D] MOL2 format, chain IB [auth I] MOL2 format, chain IA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain EA [auth C] MOL2 format, chain DB [auth H] MOL2 format, chain DA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain CA [auth C] mmCIF format, chain YB [auth L] mmCIF format, chain YA [auth G] mmCIF format, chain Y [auth B] mmCIF format, chain XB [auth L] mmCIF format, chain XA [auth G] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain TB [auth K] mmCIF format, chain TA [auth F] mmCIF format, chain SB [auth K] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth J] mmCIF format, chain OA [auth E] mmCIF format, chain NB [auth J] mmCIF format, chain NA [auth E] mmCIF format, chain JB [auth I] mmCIF format, chain JA [auth D] mmCIF format, chain IB [auth I] mmCIF format, chain IA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain EA [auth C] mmCIF format, chain DB [auth H] mmCIF format, chain DA [auth C] mmCIF format, chain CB [auth H] mmCIF format, chain CA [auth C]	CA [auth C] CB [auth H] DA [auth C] DB [auth H] EA [auth C] CA [auth C], CB [auth H], DA [auth C], DB [auth H], EA [auth C], EB [auth H], IA [auth D], IB [auth I], JA [auth D], JB [auth I], NA [auth E], NB [auth J], OA [auth E], OB [auth J], P [auth A], PA [auth E], Q [auth A], R [auth A], SB [auth K], TA [auth F], TB [auth K], V [auth B], W [auth B], X [auth B], XA [auth G], XB [auth L], Y [auth B], YA [auth G], YB [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth C] Focus chain CB [auth H] Focus chain DA [auth C] Focus chain DB [auth H] Focus chain EA [auth C] Focus chain EB [auth H] Focus chain IA [auth D] Focus chain IB [auth I] Focus chain JA [auth D] Focus chain JB [auth I] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain OA [auth E] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain R [auth A] Focus chain SB [auth K] Focus chain TA [auth F] Focus chain TB [auth K] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth G] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain YA [auth G] Focus chain YB [auth L] Interactions & Density Focus chain CA [auth C] Focus chain CB [auth H] Focus chain DA [auth C] Focus chain DB [auth H] Focus chain EA [auth C] Focus chain EB [auth H] Focus chain IA [auth D] Focus chain IB [auth I] Focus chain JA [auth D] Focus chain JB [auth I] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain OA [auth E] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain R [auth A] Focus chain SB [auth K] Focus chain TA [auth F] Focus chain TB [auth K] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth G] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain YA [auth G] Focus chain YB [auth L]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain WB [auth L] SDF format, chain WA [auth G] SDF format, chain VB [auth L] SDF format, chain VA [auth G] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain RB [auth K] SDF format, chain RA [auth F] SDF format, chain QB [auth K] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MB [auth J] SDF format, chain MA [auth E] SDF format, chain LB [auth J] SDF format, chain LA [auth E] SDF format, chain HB [auth I] SDF format, chain HA [auth D] SDF format, chain GB [auth I] SDF format, chain GA [auth D] SDF format, chain BB [auth H] SDF format, chain BA [auth C] SDF format, chain AB [auth H] SDF format, chain AA [auth C] MOL2 format, chain WB [auth L] MOL2 format, chain WA [auth G] MOL2 format, chain VB [auth L] MOL2 format, chain VA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain RB [auth K] MOL2 format, chain RA [auth F] MOL2 format, chain QB [auth K] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth J] MOL2 format, chain MA [auth E] MOL2 format, chain LB [auth J] MOL2 format, chain LA [auth E] MOL2 format, chain HB [auth I] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth I] MOL2 format, chain GA [auth D] MOL2 format, chain BB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain AA [auth C] mmCIF format, chain WB [auth L] mmCIF format, chain WA [auth G] mmCIF format, chain VB [auth L] mmCIF format, chain VA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain RB [auth K] mmCIF format, chain RA [auth F] mmCIF format, chain QB [auth K] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth J] mmCIF format, chain MA [auth E] mmCIF format, chain LB [auth J] mmCIF format, chain LA [auth E] mmCIF format, chain HB [auth I] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth I] mmCIF format, chain GA [auth D] mmCIF format, chain BB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth H] BA [auth C] BB [auth H] GA [auth D] AA [auth C], AB [auth H], BA [auth C], BB [auth H], GA [auth D], GB [auth I], HA [auth D], HB [auth I], LA [auth E], LB [auth J], MA [auth E], MB [auth J], N [auth A], O [auth A], QB [auth K], RA [auth F], RB [auth K], SA [auth F], T [auth B], U [auth B], VA [auth G], VB [auth L], WA [auth G], WB [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain GA [auth D] Focus chain GB [auth I] Focus chain HA [auth D] Focus chain HB [auth I] Focus chain LA [auth E] Focus chain LB [auth J] Focus chain MA [auth E] Focus chain MB [auth J] Focus chain N [auth A] Focus chain O [auth A] Focus chain QB [auth K] Focus chain RA [auth F] Focus chain RB [auth K] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth G] Focus chain VB [auth L] Focus chain WA [auth G] Focus chain WB [auth L] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain GA [auth D] Focus chain GB [auth I] Focus chain HA [auth D] Focus chain HB [auth I] Focus chain LA [auth E] Focus chain LB [auth J] Focus chain MA [auth E] Focus chain MB [auth J] Focus chain N [auth A] Focus chain O [auth A] Focus chain QB [auth K] Focus chain RA [auth F] Focus chain RB [auth K] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth G] Focus chain VB [auth L] Focus chain WA [auth G] Focus chain WB [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.216 (Depositor), 0.215 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.1	α = 90
b = 208.1	β = 90
c = 142.768	γ = 90

Software Package:

Software Name	Purpose
REFMAC	model building
SCALEPACK	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
REFMAC	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-04
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other