4B2H | pdb_00004b2h

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

• PDB DOI: https://doi.org/10.2210/pdb4B2H/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Halobacterium salinarum R1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-07-16 Released: 2013-05-29 
• Deposition Author(s): Yu, Y., Heidel, B., Parapugna, T.L., Wenderhold-Reeb, S., Song, B., Schoenherr, H., Grininger, M., Noell, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.178 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

The Flavoprotein Dodecin as a Redox Probe for Electron Transfer Through DNA.

Yu, Y., Heidel, B., Parapugna, T.L., Wenderhold-Reeb, S., Song, B., Schonherr, H., Grininger, M., Noll, G.

(2013) Angew Chem Int Ed Engl 52: 4950

• PubMed: 23532984 
• DOI: https://doi.org/10.1002/anie.201208987
• Primary Citation Related Structures: 
  4B2H, 4B2M

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Organizational Affiliation: 
• NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität Siegen, Fakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen, 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: 8.74 kDa 
• Atom Count: 597 
• Modeled Residue Count: 62 
• Deposited Residue Count: 74 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DODECIN	A	74	Halobacterium salinarum R1	Mutation(s): 1
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
C3F	D [auth A]	3-[7,8-dimethyl-2,4-bis(oxidanylidene)benzo[g]pteridin-10-yl]propylcarbamic acid C16 H17 N5 O4 SDVCPFDZIJESAH-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	B [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.178 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.005	α = 90
b = 142.005	β = 90
c = 142.005	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: 2013-05-29 
Deposition Author(s): Yu, Y., Heidel, B., Parapugna, T.L., Wenderhold-Reeb, S., Song, B., Schoenherr, H., Grininger, M., Noell, G.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Derived calculations, Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description