6P8L | pdb_00006p8l

Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-ray Data)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction.

Benavides, B.S.Valandro, S.Cioloboc, D.Taylor, A.B.Schanze, K.S.Kurtz Jr., D.M.

(2020) Biochemistry 59: 1618-1629

  • DOI: https://doi.org/10.1021/acs.biochem.9b01103
  • Primary Citation Related Structures: 
    6P8K, 6P8L

  • PubMed Abstract: 

    The iron storage protein bacterioferritin (Bfr) binds up to 12 hemes b at specific sites in its protein shell. The heme b can be substituted with the photosensitizer Zn(II)-protoporphyrin IX (ZnPP), and photosensitized reductive iron release from the ferric oxyhydroxide {[FeO(OH)] n } core inside the ZnPP-Bfr protein shell was demonstrated [Cioloboc, D., et al. (2018) Biomacromolecules 19 , 178-187]. This report describes the X-ray crystal structure of ZnPP-Bfr and the effects of loaded iron on the photophysical properties of the ZnPP. The crystal structure of ZnPP-Bfr shows a unique six-coordinate zinc in the ZnPP with two axial methionine sulfur ligands. Steady state and transient ultraviolet-visible absorption and luminescence spectroscopies show that irradiation with light overlapping the Soret absorption causes oxidation of ZnPP to the cation radical ZnPP •+ only when the ZnPP-Bfr is loaded with [FeO(OH)] n . Femtosecond transient absorption spectroscopy shows that this photooxidation occurs from the singlet excited state ( 1 ZnPP*) on the picosecond time scale and is consistent with two oxidizing populations of Fe 3+ , which do not appear to involve the ferroxidase center iron. We propose that [FeO(OH)] n clusters at or near the inner surface of the protein shell are responsible for ZnPP photooxidation. Hopping of the photoinjected electrons through the [FeO(OH)] n would effectively cause migration of Fe 2+ through the inner cavity to pores where it exits the protein. Reductive iron mobilization is presumed to be a physiological function of Bfrs. The phototriggered Fe 3+ reduction could be used to identify the sites of iron mobilization within the Bfr protein shell.


  • Organizational Affiliation
    • Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States.

Macromolecule Content 

  • Total Structure Weight: 229.71 kDa 
  • Atom Count: 18,117 
  • Modeled Residue Count: 1,884 
  • Deposited Residue Count: 1,896 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacterioferritin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
158Escherichia coli K-12Mutation(s): 0 
Gene Names: bfrb3336JW3298
EC: 1.16.3.1
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Explore P0ABD3 
Go to UniProtKB:  P0ABD3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABD3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZNH
(Subject of Investigation/LOI)

Query on ZNH



Download:Ideal Coordinates CCD File
AA [auth D]
GB [auth L]
IA [auth F]
R [auth B]
RA [auth H]
AA [auth D],
GB [auth L],
IA [auth F],
R [auth B],
RA [auth H],
YA [auth J]
PROTOPORPHYRIN IX CONTAINING ZN
C34 H32 N4 O4 Zn
FUTVBRXUIKZACV-RGGAHWMASA-L
MLI

Query on MLI



Download:Ideal Coordinates CCD File
AB [auth J]
BB [auth J]
CB [auth K]
DA [auth D]
EA [auth D]
AB [auth J],
BB [auth J],
CB [auth K],
DA [auth D],
EA [auth D],
EB [auth K],
FB [auth K],
GA [auth E],
HA [auth E],
IB [auth L],
JB [auth L],
LA [auth F],
MA [auth F],
O [auth A],
OA [auth G],
P [auth A],
PA [auth G],
Q [auth A],
QA [auth G],
TA [auth H],
U [auth B],
UA [auth H],
V [auth B],
W [auth B],
WA [auth I],
XA [auth I],
Y [auth C],
Z [auth C]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
BA [auth D]
DB [auth K]
FA [auth E]
HB [auth L]
JA [auth F]
BA [auth D],
DB [auth K],
FA [auth E],
HB [auth L],
JA [auth F],
M [auth A],
NA [auth G],
S [auth B],
SA [auth H],
VA [auth I],
X [auth C],
ZA [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
CA [auth D],
KA [auth F],
N [auth A],
T [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.918α = 90
b = 207.918β = 90
c = 143.046γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United States8UL1TR001120

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description