5B0U | pdb_00005b0u

Crystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ)

• PDB DOI: https://doi.org/10.2210/pdb5B0U/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Oplophorus gracilirostris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-11-04 Released: 2016-01-13 
• Deposition Author(s): Tomabechi, Y., Ehara, H., Sekine, S.I., Shirouzu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine

Tomabechi, Y., Hosoya, T., Ehara, H., Sekine, S., Shirouzu, M., Inouye, S.

(2016) Biochem Biophys Res Commun 470: 88-93

• PubMed: 26746005 
• DOI: https://doi.org/10.1016/j.bbrc.2015.12.123
• Primary Citation Related Structures: 
  5B0U


• PubMed Abstract: 
  

  The 19 kDa protein (KAZ) of Oplophorus luciferase is a catalytic component, that oxidizes coelenterazine (a luciferin) with molecular oxygen to emit light. The crystal structure of the mutated 19 kDa protein (nanoKAZ) was determined at 1.71 Å resolution. The structure consists of 11 antiparallel β-strands forming a β-barrel that is capped by 4 short α-helices. The structure of nanoKAZ is similar to those of fatty acid-binding proteins (FABPs), even though the amino acid sequence similarity was very low between them. The coelenterazine-binding site and the catalytic site for the luminescence reaction might be in a central cavity of the β-barrel structure.

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Organizational Affiliation: 
• Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
Yokohama Research Center, JNC Co., 5-1 Okawa, Kanazawa-ku, Yokohama 236-8605, Japan. Electronic address: [e-mail].

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: 43.04 kDa 
• Atom Count: 3,020 
• Modeled Residue Count: 339 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oplophorus-luciferin 2-monooxygenase catalytic subunit	A, B	191	Oplophorus gracilirostris	Mutation(s): 16  EC: 1.13.12.13
UniProt
Find proteins for Q9GV45 (Oplophorus gracilirostris) Explore Q9GV45  Go to UniProtKB:  Q9GV45

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.067	α = 90
b = 79.067	β = 90
c = 123.425	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Tomabechi, Y., Ehara, H., Sekine, S.I., Shirouzu, M.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2016-02-10
  Changes: Database references
• Version 1.3: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references