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- PDB-4e5d: 2.2A resolution structure of a firefly luciferase-benzothiazole i... -

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Basic information

Entry
Database: PDB / ID: 4e5d
Title2.2A resolution structure of a firefly luciferase-benzothiazole inhibitor complex
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE / MONOOXYGENASE / PHOTOPROTEIN / LUMINESCENCE / profiling / PubChem / luciferase / quantitative high-throughput screening / qHTS / firefly luciferase / reporter-gene assays / adenylate forming enzymes / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / 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, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(2-fluorophenyl)-6-methoxy-1,3-benzothiazole / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.201 Å
AuthorsLovell, S. / Battaile, K.P. / Throne, N. / Shen, M. / Auld, D.S. / Inglese, J.
CitationJournal: Chem.Biol. / Year: 2012
Title: Firefly luciferase in chemical biology: a compendium of inhibitors, mechanistic evaluation of chemotypes, and suggested use as a reporter.
Authors: Thorne, N. / Shen, M. / Lea, W.A. / Simeonov, A. / Lovell, S. / Auld, D.S. / Inglese, J.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)61,0782
Polymers60,8191
Non-polymers2591
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.939, 83.939, 96.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 60818.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Lyophilized power from Sigma-Aldrich Catalog# L9506
Source: (natural) Photinus pyralis (common eastern firefly) / References: UniProt: P08659, firefly luciferase
#2: Chemical ChemComp-0NJ / 2-(2-fluorophenyl)-6-methoxy-1,3-benzothiazole


Mass: 259.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10FNOS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 25% (v/v) PEG 400, 20% (v/v) PEG 3350, 0.1 M MgCl2, 0.1 M Tris, pH 8.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 10, 2009
Diffraction measurementDetails: 1.00 degrees, 12.0 sec, detector distance 150.00 mm
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.132 / Number: 159572
ReflectionResolution: 2.2→50 Å / Num. all: 34134 / Num. obs: 33216 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 8.989
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.85 / Rsym value: 0.458 / % possible all: 83
Cell measurementReflection used: 159572

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.31 Å41.99 Å
Translation2.31 Å41.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXdev_892refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCI

1lci


Resolution: 2.201→27.98 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1692 5.09 %RANDOM
Rwork0.1876 ---
obs0.1899 33214 97.36 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.901 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 63.82 Å2 / Biso mean: 25.1327 Å2 / Biso min: 7.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.3807 Å20 Å2-0 Å2
2--3.3807 Å2-0 Å2
3----6.7615 Å2
Refinement stepCycle: LAST / Resolution: 2.201→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 18 176 3478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133383
X-RAY DIFFRACTIONf_angle_d1.314598
X-RAY DIFFRACTIONf_chiral_restr0.081518
X-RAY DIFFRACTIONf_plane_restr0.007593
X-RAY DIFFRACTIONf_dihedral_angle_d13.6341202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.201-2.26570.28751390.21632191233082
2.2657-2.33880.26331200.20732406252690
2.3388-2.42230.28381310.19992638276997
2.4223-2.51930.25521510.192926422793100
2.5193-2.63380.24521210.184327142835100
2.6338-2.77260.23931720.183626652837100
2.7726-2.94610.24231250.184727032828100
2.9461-3.17330.22961510.182127012852100
3.1733-3.49210.24381470.197827002847100
3.4921-3.99620.19991400.179327112851100
3.9962-5.030.19961460.16226962842100
5.03-27.98190.22361490.204727552904100

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