1.55A structure of apo bacterioferritin from E. coli

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Monitoring and Validating Active Site Redox States in Protein Crystals.

Antonyuk, S.V.Hough, M.A.

(2011) Biochim Biophys Acta 1814: 778

  • DOI: https://doi.org/10.1016/j.bbapap.2010.12.017
  • Primary Citation of Related Structures:  
    2Y1A, 2Y3Q

  • PubMed Abstract: 

    High resolution protein crystallography using synchrotron radiation is one of the most powerful tools in modern biology. Improvements in resolution have arisen from the use of X-ray beamlines with higher brightness and flux and the development of advanced detectors. However, it is increasingly recognised that the benefits brought by these advances have an associated cost, namely deleterious effects of X-ray radiation on the sample (radiation damage). In particular, X-ray induced reduction and damage to redox centres has been shown to occur much more rapidly than other radiation damage effects, such as loss of resolution or damage to disulphide bridges. Selection of an appropriate combination of in-situ single crystal spectroscopies during crystallographic experiments, such as UV-visible absorption and X-ray absorption spectroscopy (XAFS), allows for effective monitoring of redox states in protein crystals in parallel with structure determination. Such approaches are also essential in cases where catalytic intermediate species are generated by exposure to the X-ray beam. In this article, we provide a number of examples in which multiple single crystal spectroscopies have been key to understanding the redox status of Fe and Cu centres in crystal structures. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

  • Organizational Affiliation

    Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
158Escherichia coliMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
DA [auth E]
DB [auth L]
HA [auth F]
KA [auth G]
M [auth A]
DA [auth E],
DB [auth L],
HA [auth F],
KA [auth G],
M [auth A],
NA [auth H],
P [auth B],
RA [auth I],
U [auth C],
WA [auth J],
Z [auth D],
ZA [auth K]
C34 H32 Fe N4 O4
Query on BTB

Download Ideal Coordinates CCD File 
CA [auth D],
CB [auth K],
GB [auth L],
VA [auth I]
C8 H19 N O5
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth K]
EA [auth E]
EB [auth L]
FA [auth E]
AA [auth D],
AB [auth K],
EA [auth E],
EB [auth L],
FA [auth E],
IA [auth F],
LA [auth G],
N [auth A],
OA [auth H],
PA [auth H],
Q [auth B],
R [auth B],
S [auth B],
SA [auth I],
UA [auth I],
V [auth C],
W [auth C],
X [auth C],
XA [auth J]
O4 S
Query on ACT

Download Ideal Coordinates CCD File 
BA [auth D]
BB [auth K]
FB [auth L]
GA [auth E]
JA [auth F]
BA [auth D],
BB [auth K],
FB [auth L],
GA [auth E],
JA [auth F],
MA [auth G],
O [auth A],
QA [auth H],
T [auth B],
TA [auth I],
Y [auth C],
YA [auth J]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208α = 90
b = 208β = 90
c = 142.6γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-05-19
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description