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- PDB-6q2m: Crystal structure of Photinus pyralis Luciferase Pps6 mutant in c... -

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Basic information

Entry
Database: PDB / ID: 6q2m
TitleCrystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA
ComponentsLuciferin 4-monooxygenase
KeywordsLIGASE / Luciferase / adenylation domain / Bioluminescence
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
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
Similarity search - Domain/homology
(2S,5S)-hexane-2,5-diol / 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPatel, K.D. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM116957 United States
CitationJournal: Biochemistry / Year: 2019
Title: Mutagenesis and Structural Studies Reveal the Basis for the Activity and Stability Properties That Distinguish thePhotinusLuciferasesscintillansandpyralis.
Authors: Branchini, B.R. / Fontaine, D.M. / Southworth, T.L. / Huta, B.P. / Racela, A. / Patel, K.D. / Gulick, A.M.
History
DepositionAug 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Luciferin 4-monooxygenase
B: Luciferin 4-monooxygenase
C: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,99355
Polymers183,7033
Non-polymers5,29052
Water6,143341
1
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,16721
Polymers61,2341
Non-polymers1,93220
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,56412
Polymers61,2341
Non-polymers1,32911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,26322
Polymers61,2341
Non-polymers2,02821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.268, 95.455, 152.020
Angle α, β, γ (deg.)90.000, 101.556, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 61234.438 Da / Num. of mol.: 3 / Mutation: T214N, A222C, Y255F, S276T, H332N, E354N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08659, firefly luciferase

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Non-polymers , 5 types, 393 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DYD / (2S,5S)-hexane-2,5-diol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SLU / 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE


Mass: 606.611 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H18N8O8S3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.36 % / Description: Thin rod shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.05M EPPS pH 8.5, 25% PEG4000, 2% 2,5 Hexanediol / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 93 K / Ambient temp details: 93 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.75→48.02 Å / Num. obs: 46929 / % possible obs: 96.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 44.3 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.062 / Rrim(I) all: 0.165 / Net I/σ(I): 11.8
Reflection shellResolution: 2.751→2.798 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2392 / CC1/2: 0.771 / Rpim(I) all: 0.38 / Rrim(I) all: 1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G36

4g36


Resolution: 2.75→44.7 Å / SU ML: 0.2956 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1354 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.218 1998 4.26 %
Rwork0.1942 44914 -
obs0.1952 46912 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.92 Å2
Refinement stepCycle: LAST / Resolution: 2.75→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11281 0 338 342 11961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011411845
X-RAY DIFFRACTIONf_angle_d1.071816029
X-RAY DIFFRACTIONf_chiral_restr0.06561813
X-RAY DIFFRACTIONf_plane_restr0.00672049
X-RAY DIFFRACTIONf_dihedral_angle_d8.14336941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.26091490.24893290X-RAY DIFFRACTION99.54
2.82-2.90.28691380.23783311X-RAY DIFFRACTION99.62
2.9-2.980.24991520.24223240X-RAY DIFFRACTION98.83
2.98-3.080.29161450.2363170X-RAY DIFFRACTION98.13
3.08-3.190.24951450.21823318X-RAY DIFFRACTION99.51
3.19-3.310.24161480.20313301X-RAY DIFFRACTION99.54
3.31-3.470.2571240.20532905X-RAY DIFFRACTION88.7
3.47-3.650.19391470.19793222X-RAY DIFFRACTION97.91
3.65-3.880.20971230.17272839X-RAY DIFFRACTION95.55
3.88-4.180.15671330.17213061X-RAY DIFFRACTION93.04
4.18-4.60.20131460.16353304X-RAY DIFFRACTION99.83
4.6-5.260.18461470.16593262X-RAY DIFFRACTION98.16
5.26-6.620.22461480.20863337X-RAY DIFFRACTION99.77
6.62-44.70.21991530.193354X-RAY DIFFRACTION98.76

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