7OME

Azacoelenterazine-bound Renilla-type engineered ancestral luciferase variant (AncFT7)

PDB DOI: https://doi.org/10.2210/pdb7OME/pdb

Classification: LUMINESCENT PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-21 Released: 2022-06-01
Deposition Author(s): Schenkmayerova, A., Janin, Y.L., Marek, M.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.190
R-Value Work: 0.168
R-Value Observed: 0.169

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

Structural and chemical basis of the Renilla-type bioluminescence

Schenkmayerova, A., Janin, Y., Damborsky, J., Marek, M.

To be published.

Macromolecule Content

Total Structure Weight: 36.4 kDa
Atom Count: 2,665
Modelled Residue Count: 295
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renilla-type engineered ancestral luciferase variant (AncFT7)	A	312	synthetic construct	Mutation(s): 0 EC: 1.13.12.5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VK8 (Subject of Investigation/LOI) Query on VK8 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-8-(phenylmethyl)-[1,2,4]triazolo[4,3-a]pyrazin-3-one C₂₅ H₂₀ N₄ O₃ FAFQJYQLYIUGAT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.190
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.076	α = 90
b = 64.487	β = 90
c = 98.096	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Schenkmayerova, A.

Funding Organization	Location	Grant Number
European Commission	Czech Republic	MSCA-IF-2017 792772

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 1.1: 2024-01-31
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 R01GM133198.