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- PDB-5gz2: luciferase complex with 7-cy-L -

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Basic information

Entry
Database: PDB / ID: 5gz2
Titleluciferase complex with 7-cy-L
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE / Luciferae
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / CoA-ligase activity / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding
Similarity search - Function
ANL, N-terminal domain / 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 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7BV / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSu, J. / Wang, F. / Gu, L.
CitationJournal: To Be Published
Title: luciferase complex with 7-cy-L
Authors: Su, J. / Wang, F.
History
DepositionSep 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 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)48,8942
Polymers48,5331
Non-polymers3611
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17400 Å2
Unit cell
Length a, b, c (Å)74.154, 74.154, 95.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 48532.609 Da / Num. of mol.: 1 / Fragment: UNP residues 3-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli (E. coli) / References: UniProt: P08659, firefly luciferase
#2: Chemical ChemComp-7BV / (4S)-2-[6-(azepan-1-yl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid


Mass: 361.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: Sodium malonate , PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 35023 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 51.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2→40.18 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.95
RfactorNum. reflection% reflection
Rfree0.239 1626 4.65 %
Rwork0.208 --
obs0.209 34955 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 24 141 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013480
X-RAY DIFFRACTIONf_angle_d1.1234723
X-RAY DIFFRACTIONf_dihedral_angle_d14.9722080
X-RAY DIFFRACTIONf_chiral_restr0.06526
X-RAY DIFFRACTIONf_plane_restr0.007609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.0580.31261090.25992840X-RAY DIFFRACTION99
2.058-2.12440.29041350.26642718X-RAY DIFFRACTION100
2.1244-2.20030.34561070.26272787X-RAY DIFFRACTION100
2.2003-2.28840.3421380.25542749X-RAY DIFFRACTION100
2.2884-2.39250.34771560.2532764X-RAY DIFFRACTION100
2.3925-2.51870.29971280.24552758X-RAY DIFFRACTION100
2.5187-2.67640.24961670.23332752X-RAY DIFFRACTION100
2.6764-2.8830.30441210.22672799X-RAY DIFFRACTION100
2.883-3.17310.25241290.22732771X-RAY DIFFRACTION100
3.1731-3.6320.22611540.21352766X-RAY DIFFRACTION100
3.632-4.57480.20991320.17652812X-RAY DIFFRACTION100
4.5748-40.1910.18461500.17292813X-RAY DIFFRACTION100

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