4B2J

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

PDB DOI: https://doi.org/10.2210/pdb4B2J/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.186
R-Value Work: 0.165
R-Value Observed: 0.166

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 9.11 kDa
Atom Count: 616
Modelled Residue Count: 64
Deposited Residue Count: 76
Unique protein chains: 1

Macromolecules

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(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] mmCIF 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] mmCIF 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] mmCIF 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] mmCIF format, chain B [auth A] mmCIF 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] mmCIF 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
4FW Query on 4FW	A	L-PEPTIDE LINKING	C₁₁ H₁₁ F N₂ O₂		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.186
R-Value Work: 0.165
R-Value Observed: 0.166
Space Group: F 4₁ 3 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 142.9	α = 90
b = 142.9	β = 90
c = 142.9	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-17

Deposition Author(s):

Revision History (Full details and data files)

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

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Deposit Data

Help and Resources

4B2J

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

Directed Manipulation of a Flavoprotein Photocycle.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)