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- PDB-3iep: Firefly luciferase apo structure (P41 form) -

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Basic information

Entry
Database: PDB / ID: 3iep
TitleFirefly luciferase apo structure (P41 form)
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / PHOTOPROTEIN / LUMINESCENCE / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Peroxisome
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
Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLovell, S. / Battaile, K.P. / Auld, D.S. / Thorne, N. / Lea, W.A. / Maloney, D.J. / Shen, M. / Raj, G. / Thomas, C.J. / Simeonov, A. ...Lovell, S. / Battaile, K.P. / Auld, D.S. / Thorne, N. / Lea, W.A. / Maloney, D.J. / Shen, M. / Raj, G. / Thomas, C.J. / Simeonov, A. / Hanzlik, R.P. / Inglese, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124.
Authors: Auld, D.S. / Lovell, S. / Thorne, N. / Lea, W.A. / Maloney, D.J. / Shen, M. / Rai, G. / Battaile, K.P. / Thomas, C.J. / Simeonov, A. / Hanzlik, R.P. / Inglese, J.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Luciferin 4-monooxygenase


Theoretical massNumber of molelcules
Total (without water)60,9181
Polymers60,9181
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.685, 84.685, 96.837
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: 60918.086 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG 1500, 8% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 13, 2009
Diffraction measurementDetails: 1.00 degrees, 12.0 sec, detector distance 150.00 mm
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.132 / Number: 202033
ReflectionResolution: 2.1→50 Å / Num. obs: 39872 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 11.343
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.748 / Rsym value: 0.518 / % possible all: 100
Cell measurementReflection used: 202033

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.38 Å29.83 Å
Translation2.38 Å29.83 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.524 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2000 5 %RANDOM
Rwork0.188 ---
obs0.189 39872 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.45 Å2 / Biso mean: 31.12 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 0 199 3549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223436
X-RAY DIFFRACTIONr_bond_other_d0.0010.023137
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9624664
X-RAY DIFFRACTIONr_angle_other_deg1.61337298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69724.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04215568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6351515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
X-RAY DIFFRACTIONr_mcbond_it0.9111.52135
X-RAY DIFFRACTIONr_mcbond_other0.2261.5868
X-RAY DIFFRACTIONr_mcangle_it1.62623456
X-RAY DIFFRACTIONr_scbond_it2.32531301
X-RAY DIFFRACTIONr_scangle_it3.7284.51206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1540.2641520.2162786294499.796
2.154-2.2130.2821410.222740288299.965
2.213-2.2770.3121230.282621276099.42
2.277-2.3470.2271180.22597271899.89
2.347-2.4240.2331410.17824842625100
2.424-2.5090.231190.17523802499100
2.509-2.6040.2131160.17923572473100
2.604-2.710.2381260.182246237399.958
2.71-2.830.2161350.1762114225099.956
2.83-2.9670.2311360.18320202156100
2.967-3.1270.1911010.17619742075100
3.127-3.3160.2191070.18518451952100
3.316-3.5440.195880.18917311819100
3.544-3.8260.219950.1716151710100
3.826-4.1890.204760.1681503158099.937
4.189-4.6790.151720.14913521424100
4.679-5.3950.224620.1631205126899.921
5.395-6.5890.222460.2131034108199.907
6.589-9.2380.228340.21281484999.882
9.238-500.204120.24445448396.48

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