6FRI | pdb_00006fri

Structure of LuxB from Photobacterium leiognathi

PDB DOI: https://doi.org/10.2210/pdb6FRI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Photobacterium leiognathi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-15 Released: 2018-02-28
Deposition Author(s): Uhl, M., Gruber, K.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.271 (Depositor), 0.198 (DCC)
R-Value Work:
0.221 (Depositor)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of LuxB from Photobacterium leiognathi

Uhl, M., Gruber, K.

To be published.

Macromolecule Content

Total Structure Weight: 149.64 kDa
Atom Count: 10,952
Modeled Residue Count: 1,290
Deposited Residue Count: 1,300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkanal monooxygenase beta chain	A, B, C, D	325	Photobacterium leiognathi	Mutation(s): 0 Gene Names: luxB EC: 1.14.14.3
UniProt
Find proteins for P09141 (Photobacterium leiognathi) Explore P09141 Go to UniProtKB: P09141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09141
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.271 (Depositor), 0.198 (DCC)
R-Value Work: 0.221 (Depositor)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.324	α = 93.38
b = 52.487	β = 90.12
c = 157.662	γ = 114.14

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	--

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2018-04-04
Changes: Author supporting evidence, Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description

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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.