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- PDB-3rix: 1.7A resolution structure of a firefly luciferase-Aspulvinone J i... -

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Basic information

Entry
Database: PDB / ID: 3rix
Title1.7A resolution structure of a firefly luciferase-Aspulvinone J inhibitor complex
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / oxidoreductase / monooxygenase / photoprotein / luminescence / aspulvinone / natural product extracts / 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 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-923 / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsLovell, S. / Battaile, K.P. / Lopez, P.C. / Auld, D.S. / Schultz, P.J. / MacArthur, R. / Shen, M. / Tamayo, G. / Inglese, J. / Sherman, D.H.
CitationJournal: Chem.Biol. / Year: 2011
Title: Titration-based screening for evaluation of natural product extracts: identification of an aspulvinone family of luciferase inhibitors.
Authors: Cruz, P.G. / Auld, D.S. / Schultz, P.J. / Lovell, S. / Battaile, K.P. / MacArthur, R. / Shen, M. / Tamayo-Castillo, G. / Inglese, J. / Sherman, D.H.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Dec 5, 2012Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2832
Polymers60,8191
Non-polymers4651
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.738, 83.738, 96.913
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 / Source: (natural) Photinus pyralis (common eastern firefly) / References: UniProt: P08659, firefly luciferase
#2: Chemical ChemComp-923 / (5Z)-4-hydroxy-3-[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]-5-{[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]methylidene}furan-2(5H)-one / Aspulvinone J-CR


Mass: 464.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→96.91 Å / Num. all: 73404 / Num. obs: 73404 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.86 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7544
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.7-1.796.880.862.287336410661100
1.79-1.96.70.513.746777910121100
1.9-2.037.070.296.57672709515100
2.03-2.196.790.1710.32600128837100
2.19-2.46.940.1115.54565798157100
2.4-2.697.020.0821.46519647400100
2.69-3.16.760.0531.2144002650999.98
3.1-3.86.950.0348.0638351551599.95
3.8-5.386.590.0361.0528329429899.96
5.38-96.916.560.0360.4715694239199.93

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
PHENIXdev_605refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3IES

3ies


Resolution: 1.7→38.435 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.23 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 3695 5.04 %RANDOM
Rwork0.1899 ---
obs0.1913 73350 99.98 %-
all-73350 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.247 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso max: 75.14 Å2 / Biso mean: 28.3361 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1-3.2211 Å20 Å2-0 Å2
2--3.2211 Å20 Å2
3----6.4423 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 34 283 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013482
X-RAY DIFFRACTIONf_angle_d1.364747
X-RAY DIFFRACTIONf_chiral_restr0.081533
X-RAY DIFFRACTIONf_plane_restr0.006609
X-RAY DIFFRACTIONf_dihedral_angle_d15.8991264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.7-1.72240.35021440.3144265027942650
1.7224-1.7460.36231390.3076267228112672
1.746-1.77090.29411540.2779264828022648
1.7709-1.79730.311450.2483267528202675
1.7973-1.82540.29081330.2504269728302697
1.8254-1.85540.27671430.2178265728002657
1.8554-1.88730.23581220.2162269228142692
1.8873-1.92170.23811430.1976265728002657
1.9217-1.95860.22881450.2022267128162671
1.9586-1.99860.21451470.1828266628132666
1.9986-2.04210.23051580.183267828362678
2.0421-2.08960.21831440.1771266428082664
2.0896-2.14180.18631400.1708265327932653
2.1418-2.19970.22021720.1728266928412669
2.1997-2.26440.2081350.1711268428192684
2.2644-2.33750.21051210.1695268028012680
2.3375-2.4210.22021370.1658268528222685
2.421-2.5180.1981350.174269828332698
2.518-2.63250.2061480.1707266428122664
2.6325-2.77130.20781440.1679268328272683
2.7713-2.94490.20681380.1773267528132675
2.9449-3.17210.21521300.1811271528452715
3.1721-3.49120.21061530.1991268328362683
3.4912-3.99590.20291490.1762268328322683
3.9959-5.03260.19881320.1738270528372705
5.0326-38.44520.22021440.2276275128952751

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