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- PDB-3qya: Crystal structure of a red-emitter mutant of Lampyris turkestanic... -

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Basic information

Entry
Database: PDB / ID: 3qya
TitleCrystal structure of a red-emitter mutant of Lampyris turkestanicus luciferase
ComponentsLuciferase
KeywordsOXIDOREDUCTASE / bioluminescence / light emitting / mutagenesis / acyl-coenzyme A ligase / ATP binding / Luciferin-binding / Peroxisome
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome
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
DI(HYDROXYETHYL)ETHER / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesLampyris turkestanicus (Iranian firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 Å
AuthorsKheirabadi, M. / Gohlke, U. / Hossein Khani, S. / Heinemann, U. / Naderi-Manesh, H.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Crystal structure of native and a mutant of Lampyris turkestanicus luciferase implicate in bioluminescence color shift.
Authors: Kheirabadi, M. / Sharafian, Z. / Naderi-Manesh, H. / Heineman, U. / Gohlke, U. / Hosseinkhani, S.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Sep 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_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: Luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,20614
Polymers64,3251
Non-polymers88113
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.009, 85.009, 97.097
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 Luciferase


Mass: 64324.980 Da / Num. of mol.: 1 / Mutation: E354R, H431Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lampyris turkestanicus (Iranian firefly)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5UFR2, firefly luciferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDNG TO THE AUTHORS THE ELECTRON DENSITY FOR RESIDUE 268 IS UNAMBIGUOUS, AND IT CLEARLY SHOWS A ...ACCORDNG TO THE AUTHORS THE ELECTRON DENSITY FOR RESIDUE 268 IS UNAMBIGUOUS, AND IT CLEARLY SHOWS A PHENYLALANINE SIDE CHAIN. THIS RESIDUE IS ALSO A PHE IN ALL OTHER KNOWN LUCIFERASES, SO IT COULD HAVE BEEN AN ORIGINAL SEQUENCING ERROR OR IT SHOWS A SPONTANEOUS MUTATION.

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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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4 % w/v PEG 8000, 14 % v/v Ethylenglycol, 100 mM Na-HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 8, 2009 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.13→32.37 Å / Num. obs: 38301 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.756 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.13-2.190.6442.512830276897.2
2.19-2.250.6252.813794274099.9
2.25-2.310.5293.313315267799.7
2.31-2.390.4283.8132052598100
2.39-2.460.3784.3128412515100
2.46-2.550.3454.8124272440100
2.55-2.650.2955.6120602370100
2.65-2.760.2416.911467228099.9
2.76-2.880.1978.3110992169100
2.88-3.020.15710.2107422101100
3.02-3.180.12612.5100701971100
3.18-3.370.09815.89615187899.9
3.37-3.610.07820.18850176799.9
3.61-3.90.06125.68254165799.8
3.9-4.270.05328.37567151299.8
4.27-4.770.04433.66933137699.9
4.77-5.510.04233.161301201100
5.51-6.750.04928.25247103499.9
6.75-9.540.03140.1405080999.9
9.540.02153.4208143897.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.98 Å
Translation2.5 Å31.98 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BA3

1ba3


Resolution: 2.13→31.98 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.1809 / WRfactor Rwork: 0.1471 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.906 / SU B: 6.889 / SU ML: 0.08 / SU R Cruickshank DPI: 0.0326 / SU Rfree: 0.0311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1915 5 %RANDOM
Rwork0.1651 ---
obs0.1672 38301 99.6 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso max: 67.09 Å2 / Biso mean: 23.5514 Å2 / Biso min: 6.74 Å2
Baniso -1Baniso -2Baniso -3
1-6.01 Å20 Å20 Å2
2--6.01 Å20 Å2
3----12.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 2.13→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 57 419 3826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223515
X-RAY DIFFRACTIONr_bond_other_d0.0010.022451
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.974736
X-RAY DIFFRACTIONr_angle_other_deg0.94635969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88123.684152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8315591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.271518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
X-RAY DIFFRACTIONr_mcbond_it0.921.52142
X-RAY DIFFRACTIONr_mcbond_other0.2481.5872
X-RAY DIFFRACTIONr_mcangle_it1.62823466
X-RAY DIFFRACTIONr_scbond_it2.53331373
X-RAY DIFFRACTIONr_scangle_it3.9014.51265
LS refinement shellResolution: 2.133→2.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 135 -
Rwork0.179 2575 -
all-2710 -
obs--95.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1403-0.01610.10270.13320.01260.53980.0038-0.00510.02240.08610.01080.0020.0343-0.0433-0.01460.0797-0.01490.00060.04070.01570.050936.174420.123964.2558
22.729-1.75020.93710.9961-1.93433.7805-0.0999-0.13160.15290.0998-0.005-0.1034-0.22120.00360.10490.10420.0060.00140.0336-0.0170.039833.327131.669274.6049
30.26280.1586-0.0980.3103-0.01690.56350.0060.03360.0240.00590.006-0.02930.1010.0142-0.0120.08490.0019-0.01350.03-0.00530.055243.207115.307459.2071
40.6047-0.43440.53830.7950.16521.3037-0.04640.00510.0215-0.060.0264-0.01720.05960.02090.02010.0485-0.00810.01010.05040.01350.059443.756627.621539.6348
50.1985-0.2946-0.50250.68490.5311.5340.0140.0216-0.0229-0.01-0.05290.02680.1762-0.03070.03890.1492-0.0172-0.00270.0002-0.01380.033837.4591.708143.0177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 151
2X-RAY DIFFRACTION2A152 - 173
3X-RAY DIFFRACTION3A174 - 264
4X-RAY DIFFRACTION4A265 - 337
5X-RAY DIFFRACTION5A338 - 435

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