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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.250 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

To be determined

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DKA	C [auth A], D [auth B]	DECANOIC ACID C10 H20 O2 GHVNFZFCNZKVNT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.250 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.200 (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

Entry History 

Deposition Data

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

Revision History  

• 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