4B2K

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

• PDB DOI: https://doi.org/10.2210/pdb4B2K/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Halobacterium salinarum R1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-16 Released: 2013-07-17 
• Deposition Author(s): Staudt, H., Hoesl, M., Dreuw, A., Serdjukow, S., Oesterhelt, D., Budisa, N., Wachtveitl, J., Grininger, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Directed Manipulation of a Flavoprotein Photocycle.

Staudt, H., Hoesl, M.G., Dreuw, A., Serdjukow, S., Oesterhelt, D., Budisa, N., Wachtveitl, J., Grininger, M.

(2013) Angew Chem Int Ed Engl 52: 8463

• PubMed: 23818044 
• DOI: https://doi.org/10.1002/anie.201302334
• Primary Citation of Related Structures:  
  4B2J, 4B2K

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Organizational Affiliation: 

Institut für Physikalische and Theoretische Chemie, Exzellenzcluster Makromolekulare Komplexe, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 9.11 kDa 
• Atom Count: 630 
• Modelled Residue Count: 64 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DODECIN	A	76	Halobacterium salinarum R1	Mutation(s): 0
UniProt
Find proteins for B0R5M0 (Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1)) Explore B0R5M0  Go to UniProtKB:  B0R5M0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RBF	G [auth A]	RIBOFLAVIN C17 H20 N4 O6 AUNGANRZJHBGPY-SCRDCRAPSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4IN	A	L-PEPTIDE LINKING	C11 H13 N3 O2		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.301	α = 90
b = 142.301	β = 90
c = 142.301	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Staudt, H., Hoesl, M., Dreuw, A., Serdjukow, S., Oesterhelt, D., Budisa, N., Wachtveitl, J., Grininger, M.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary