4B2M

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

PDB DOI: https://doi.org/10.2210/pdb4B2M/pdb

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

Deposited: 2012-07-16 Released: 2013-05-29
Deposition Author(s): Staudt, H., Hoesl, M., Dreuw, A., Serdjukow, S., Oesterhelt, D., Budisa, N., Wachtveitl, J., Grininger, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.185
R-Value Work: 0.165
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

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: 4950-4953

PubMed: 23532984 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.201208987
Primary Citation of Related Structures:
4B2H, 4B2M

Organizational Affiliation

NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität Siegen, Fakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen, Germany.

Macromolecule Content

Total Structure Weight: 9.09 kDa
Atom Count: 598
Modelled Residue Count: 64
Deposited Residue Count: 76
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0R5M0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RBF Query on RBF Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4AW Query on 4AW	A	L-PEPTIDE LINKING	C₁₀ H₁₁ N₃ O₂		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.185
R-Value Work: 0.165
R-Value Observed: 0.166
Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.574	α = 90
b = 142.574	β = 90
c = 142.574	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 2.0: 2019-04-24
Changes: Data collection, Database references, Derived calculations, Other, Polymer sequence
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

4B2M

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

The flavoprotein dodecin as a redox probe for electron transfer through DNA.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)