5TRX

Room temperature structure of an extradiol ring-cleaving dioxygenase from B.fuscum determined using serial femtosecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb5TRX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brevibacterium fuscum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-27 Released: 2017-03-22 
• Deposition Author(s): Kovaleva, E.G., Oberthuer, D., Tolstikova, A., Mariani, V.
• Funding Organization(s): SLAC LDRD program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.232 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Double-flow focused liquid injector for efficient serial femtosecond crystallography

Oberthuer, D., Knoska, J., Wiedorn, M.O., Beyerlein, K.R., Bushnell, D.A., Kovaleva, E.G., Heymann, M., Gumprecht, L., Kirian, R.A., Barty, A., Mariani, V., Tolstikova, A., Adriano, L., Awel, S., Barthelmess, M., Dorner, K., Xavier, P.L., Yefanov, O., James, D.R., Nelson, G., Wang, D., Calvey, G., Chen, Y., Schmidt, A., Szczepek, M., Frielingsdorf, S., Lenz, O., Snell, E., Robinson, P.J., Sarler, B., Belsak, G., Macek, M., Wilde, F., Aquila, A., Boutet, S., Liang, M., Hunter, M.S., Scheerer, P., Lipscomb, J.D., Weierstall, U., Kornberg, R.D., Spence, J.C.H., Pollack, L., Chapman, H.N., Bajt, S.

(2017) Sci Rep 7: 44628

• DOI: https://doi.org/10.1038/srep44628

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 167.43 kDa 
• Atom Count: 12,065 
• Modelled Residue Count: 1,434 
• Deposited Residue Count: 1,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoprotocatechuate 2,3-dioxygenase	A, B, C, D	365	Brevibacterium fuscum	Mutation(s): 0
UniProt
Find proteins for Q45135 (Brevibacterium fuscum) Explore Q45135  Go to UniProtKB:  Q45135

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	E [auth A], G [auth B], J [auth C], L [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], I [auth B], K [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.232 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.57	α = 90
b = 154.86	β = 90
c = 101.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystFEL	data scaling
CrystFEL	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Kovaleva, E.G., Oberthuer, D., Tolstikova, A., Mariani, V.

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Funding Organization	Location	Grant Number
SLAC LDRD program	United States	--

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Data collection
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description