7ZQU | pdb_00007zqu

A fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - C72A mutant

PDB DOI: https://doi.org/10.2210/pdb7ZQU/pdb

Classification: SIGNALING PROTEIN
Organism(s): Dinoroseobacter shibae DFL 12 = DSM 16493
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2022-05-03 Released: 2023-05-17
Deposition Author(s): Batra-Safferling, R., Granzin, J.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - C72A mutant

Batra-Safferling, R., Granzin, J.

To be published.

Macromolecule Content

Total Structure Weight: 17.29 kDa
Atom Count: 1,004
Modeled Residue Count: 117
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative blue-light photoreceptor	A	146	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 1 Gene Names: Dshi_2006
UniProt
Find proteins for A8LP63 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LP63 Go to UniProtKB: A8LP63
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LP63
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.454	α = 90
b = 28.21	β = 119.397
c = 48.018	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-17

Deposition Author(s):

Batra-Safferling, R.

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	FKZ 031A16

Revision History (Full details and data files)

Version 1.0: 2023-05-17
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.