5IBO | pdb_00005ibo

1.95A resolution structure of NanoLuc luciferase

PDB DOI: https://doi.org/10.2210/pdb5IBO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Oplophorus gracilirostris
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-02-22 Released: 2016-04-13
Deposition Author(s): Lovell, S., Mehzabeen, N., Battaile, K.P., Wood, M.G., Encell, L.P., Wood, K.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.250 (Depositor), 0.257 (DCC)
R-Value Work:
0.188 (Depositor), 0.198 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

To be determined

Lovell, S., Mehzabeen, N., Battaile, K.P., Wood, M.G., Encell, L.P., Wood, K.V.

To be published.

Macromolecule Content

Total Structure Weight: 39.2 kDa
Atom Count: 2,670
Modeled Residue Count: 335
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oplophorus-luciferin 2-monooxygenase catalytic subunit	A, B	174	Oplophorus gracilirostris	Mutation(s): 16 EC: 1.13.12.13
UniProt
Find proteins for Q9GV45 (Oplophorus gracilirostris) Explore Q9GV45 Go to UniProtKB: Q9GV45
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GV45
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DKA Query on DKA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	DECANOIC ACID C₁₀ H₂₀ O₂ GHVNFZFCNZKVNT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.250 (Depositor), 0.257 (DCC)
R-Value Work: 0.188 (Depositor), 0.198 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.436	α = 90
b = 62.658	β = 90
c = 96.835	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-04-03
Changes: 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.