4W8O | pdb_00004w8o

Structure of the luciferase-like enzyme from the nonluminescent Zophobas morio mealworm

• PDB DOI: https://doi.org/10.2210/pdb4W8O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zophobas atratus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-25 Released: 2015-10-21 
• Deposition Author(s): Santos, C.R., Prado, R.A., Viviani, V., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Structure of the luciferase-like enzyme from the nonluminescent Zophobas morio mealworm

Santos, C.R., Prado, R.A., Viviani, V., Murakami, M.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.57 kDa 
• Atom Count: 7,057 
• Modeled Residue Count: 841 
• Deposited Residue Count: 854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
luciferase-like enzymeAMP-CoA-ligase	A, B	427	Zophobas atratus	Mutation(s): 0
UniProt
Find proteins for A0A0R4I967 (Zophobas atratus) Explore A0A0R4I967  Go to UniProtKB:  A0A0R4I967

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	C [auth A], E [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.774	α = 90
b = 91.005	β = 90
c = 110.294	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Santos, C.R., Prado, R.A., Viviani, V., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2012/04857-0

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Structure summary