8I11

Crystal structure of LOV1 domain of phototropin from Klebsormidium nitens

PDB DOI: https://doi.org/10.2210/pdb8I11/pdb

Classification: FLAVOPROTEIN
Organism(s): Klebsormidium nitens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-12 Released: 2024-01-24
Deposition Author(s): Gautam, A.K., Sharma, S., Gourinath, S., Kateriya, S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.221
R-Value Work: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of LOV1 domain of phototropin from klebsormidium nitens

Gautam, A.K., Sharma, S., Gourinath, S., kateria, S.

To be published.

Macromolecule Content

Total Structure Weight: 17.47 kDa
Atom Count: 1,060
Modelled Residue Count: 128
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phototropin	A	153	Klebsormidium nitens	Mutation(s): 0 Gene Names: KFL_000480260
UniProt
Find proteins for A0A1Y1HNG4 (Klebsormidium nitens) Explore A0A1Y1HNG4 Go to UniProtKB: A0A1Y1HNG4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y1HNG4
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]	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: 1.85 Å
R-Value Free: 0.221
R-Value Work: 0.193
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.868	α = 90
b = 53.868	β = 90
c = 137.014	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	India	--

Revision History (Full details and data files)

Version 1.0: 2024-01-24
Type: Initial release

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 R01GM133198.