7QXR | pdb_00007qxr

Azacoelenterazine-bound Renilla-type luciferase (AncFT)

PDB DOI: https://doi.org/10.2210/pdb7QXR/pdb

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

Deposited: 2022-01-27 Released: 2022-12-07
Deposition Author(s): Marek, M., Schenkmayerova, A., Janin, Y.L.
Funding Organization(s): Czech Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.247 (Depositor), 0.248 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Catalytic mechanism for Renilla-type luciferases

Schenkmayerova, A., Toul, M., Pluskal, D., Baatallah, R., Gagnot, G., Pinto, G.P., Santana, V.T., Stuchla, M., Neugebauer, P., Chaiyen, P., Damborsky, J., Bednar, D., Janin, Y.L., Prokop, Z., Marek, M.

(2023) Nat Catal

DOI: https://doi.org/10.1038/s41929-022-00895-z

Macromolecule Content

Total Structure Weight: 103.21 kDa
Atom Count: 7,571
Modeled Residue Count: 882
Deposited Residue Count: 885
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)	A, B, C	295	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NSW (Subject of Investigation/LOI) Query on NSW Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	3-(4-hydroxyphenyl)-8-[(4-hydroxyphenyl)methyl]-5-(phenylmethyl)-1$l^{4},4,7,8-tetrazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one C₂₅ H₂₁ N₄ O₃ FAFQJYQLYIUGAT-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.247 (Depositor), 0.248 (DCC)
R-Value Work: 0.192 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.284	α = 90
b = 87.549	β = 93.46
c = 102.693	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-07

Deposition Author(s):

Schenkmayerova, A.

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	22-09853S

Revision History (Full details and data files)

Version 1.0: 2022-12-07
Type: Initial release
Version 1.1: 2023-01-18
Changes: Database references
Version 1.2: 2024-01-31
Changes: Data collection, 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.