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- PDB-3ier: Firefly luciferase apo structure (P41 form) with PEG 400 bound -

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Basic information

Entry
Database: PDB / ID: 3ier
TitleFirefly luciferase apo structure (P41 form) with PEG 400 bound
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 / AMP-binding enzyme, C-terminal domain superfamily / 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: 2.05 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 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)61,1122
Polymers60,9181
Non-polymers1941
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.233, 84.233, 96.905
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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 25% PEG 400, 20% PEG 3350, 0.1M MgCl2, 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: 0.123 / Number: 207798
ReflectionResolution: 2.05→50 Å / Num. obs: 42128 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 11.075
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.19 / Rsym value: 0.479 / % possible all: 98.7
Cell measurementReflection used: 207798

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.23 Å26.97 Å
Translation2.23 Å26.97 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
Starting model: PDB entry 3IEP

3iep


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.349 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2129 5.1 %RANDOM
Rwork0.183 ---
obs0.185 42128 99.42 %-
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: 64.32 Å2 / Biso mean: 23.931 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 10 197 3567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223454
X-RAY DIFFRACTIONr_bond_other_d00.023171
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9644685
X-RAY DIFFRACTIONr_angle_other_deg0.81637388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50624.161149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9415579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9041515
X-RAY DIFFRACTIONr_chiral_restr0.1150.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213817
X-RAY DIFFRACTIONr_gen_planes_other00.02700
X-RAY DIFFRACTIONr_mcbond_it1.1951.52139
X-RAY DIFFRACTIONr_mcbond_other0.3241.5869
X-RAY DIFFRACTIONr_mcangle_it2.05723467
X-RAY DIFFRACTIONr_scbond_it2.88831315
X-RAY DIFFRACTIONr_scangle_it4.5594.51213
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 (%)
2.05-2.1040.2461660.212798310195.582
2.104-2.1620.2481610.22875305799.313
2.162-2.2240.2781590.22753292499.59
2.224-2.2920.2241360.1812756290299.655
2.292-2.3670.2111260.172612275299.491
2.367-2.450.1991240.1582557268899.74
2.45-2.5430.2341270.1752477260999.808
2.543-2.6460.2411190.172394251899.801
2.646-2.7630.2331410.172240238499.874
2.763-2.8980.2481200.1812224234799.872
2.898-3.0540.2641160.1892038215699.907
3.054-3.2390.247960.18819832079100
3.239-3.4610.226870.1911857194599.949
3.461-3.7370.19940.17117211815100
3.737-4.0910.196930.16415851678100
4.091-4.570.214800.1641442152499.869
4.57-5.270.182700.16812671337100
5.27-6.4370.211560.20710961152100
6.437-9.0280.25400.228841881100
9.028-500.223180.24248352395.794

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