Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 79.78 kDa 
• Atom Count: 6133 
• Modelled Residue Count: 723 
• Deposited Residue Count: 724 
• Unique protein chains: 1

6I8O

Dye type peroxidase Aa from Streptomyces lividans: 39.2kGy structure

• PDB DOI: 10.2210/pdb6I8O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces lividans TK24
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-20 Released: 2019-07-31 
• Deposition Author(s): Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.235 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins.

Ebrahim, A., Moreno-Chicano, T., Appleby, M.V., Chaplin, A.K., Beale, J.H., Sherrell, D.A., Duyvesteyn, H.M.E., Owada, S., Tono, K., Sugimoto, H., Strange, R.W., Worrall, J.A.R., Axford, D., Owen, R.L., Hough, M.A.

(2019) IUCrJ 6: 543-551

• PubMed: 31316799 
• DOI: 10.1107/S2052252519003956
• Primary Citation of Related Structures:  
  6I43, 6I7Z, 6I8E, 6I8I, 6I8J, 6I8K, 6I8O, 6I8P, 6I8Q, 6IBN, 6Q31, 6Q34, 6Q3D, 6Q3E


• PubMed Abstract: 
  

An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.

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Organizational Affiliation: 

School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deferrochelatase/peroxidase	A, B	362	Streptomyces lividans TK24	Mutation(s): 0  Gene Names: SLIV_26340 EC: 1.11.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.235 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.99	α = 90
b = 68.359	β = 105.63
c = 74.946	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
cctbx.prime	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-11-20 
• Released Date: 2019-07-31 
Deposition Author(s): Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L.

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Database references