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- PDB-5wys: luciferase with inhibitor 3i -

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Basic information

Entry
Database: PDB / ID: 5wys
Titleluciferase with inhibitor 3i
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / luciferase / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / long-chain fatty acid-CoA ligase activity / fatty-acyl-CoA biosynthetic process / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-7V6 / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.999 Å
AuthorsGu, L. / Su, J. / Wang, F.
CitationJournal: Anal. Chem. / Year: 2017
Title: Inhibiting Firefly Bioluminescence by Chalcones
Authors: Zhang, H. / Su, J. / Lin, Y. / Bai, H. / Liu, J. / Chen, H. / Du, L. / Gu, L. / Li, M.
History
DepositionJan 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1032
Polymers60,8191
Non-polymers2841
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22420 Å2
Unit cell
Length a, b, c (Å)118.141, 118.141, 96.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 60818.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08659, firefly luciferase
#2: Chemical ChemComp-7V6 / 5-[(3R)-3-(4-boranylphenyl)-3-oxidanyl-propyl]-2-oxidanyl-benzoic acid


Mass: 284.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17BO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8 / Details: 0.5 M Li2SO4, 15% PEG8000, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: MACSCIENCE / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.999→44.55 Å / Num. obs: 14133 / % possible obs: 100 % / Redundancy: 0.1285 % / Net I/σ(I): 25.53

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2124: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementResolution: 2.999→44.547 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2696 1416 10.02 %
Rwork0.1954 --
obs0.2029 14133 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.999→44.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 21 0 4226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014321
X-RAY DIFFRACTIONf_angle_d1.1425854
X-RAY DIFFRACTIONf_dihedral_angle_d15.5262583
X-RAY DIFFRACTIONf_chiral_restr0.063660
X-RAY DIFFRACTIONf_plane_restr0.007752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9988-3.1060.3771390.22981248X-RAY DIFFRACTION99
3.106-3.23030.35961370.24921232X-RAY DIFFRACTION100
3.2303-3.37730.38741380.24381250X-RAY DIFFRACTION100
3.3773-3.55520.33551390.21341256X-RAY DIFFRACTION100
3.5552-3.77790.29061390.19221248X-RAY DIFFRACTION100
3.7779-4.06940.25411410.18271264X-RAY DIFFRACTION100
4.0694-4.47860.21041410.16481269X-RAY DIFFRACTION100
4.4786-5.12580.21591420.16041281X-RAY DIFFRACTION100
5.1258-6.45490.2411450.20311300X-RAY DIFFRACTION100
6.4549-44.55170.25561550.19761369X-RAY DIFFRACTION99

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