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- PDB-6hps: Near-infrared dual bioluminescence imaging in vivo using infra-lu... -

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Basic information

Entry
Database: PDB / ID: 6hps
TitleNear-infrared dual bioluminescence imaging in vivo using infra-luciferin
ComponentsLuciferin 4-monooxygenase
KeywordsFLUORESCENT PROTEIN / near-infrared Bioluminescence imaging / P. pyralis luciferase / ANL SUPERFAMILY / LIGASE / ADENYLATING ENZYMES / LUCIFERASE / DOMAIN ALTERNATION
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, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
Chem-GKH / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsParkinson, G.N. / Stowe, C. / Anderson, J.C.
CitationJournal: Elife / Year: 2019
Title: Near-infrared dual bioluminescence imaging in mouse models of cancer using infraluciferin.
Authors: Stowe, C.L. / Burley, T.A. / Allan, H. / Vinci, M. / Kramer-Marek, G. / Ciobota, D.M. / Parkinson, G.N. / Southworth, T.L. / Agliardi, G. / Hotblack, A. / Lythgoe, M.F. / Branchini, B.R. / ...Authors: Stowe, C.L. / Burley, T.A. / Allan, H. / Vinci, M. / Kramer-Marek, G. / Ciobota, D.M. / Parkinson, G.N. / Southworth, T.L. / Agliardi, G. / Hotblack, A. / Lythgoe, M.F. / Branchini, B.R. / Kalber, T.L. / Anderson, J.C. / Pule, M.A.
History
DepositionSep 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,2354
Polymers119,9702
Non-polymers1,2652
Water0
1
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6182
Polymers59,9851
Non-polymers6331
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6182
Polymers59,9851
Non-polymers6331
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.509, 114.016, 101.557
Angle α, β, γ (deg.)90.000, 98.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 59984.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P08659, firefly luciferase
#2: Chemical ChemComp-GKH / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate


Mass: 632.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N8O8S3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.27 Å3/Da / Density % sol: 45.79 % / Description: Thin flat plate
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2017
RadiationMonochromator: single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.1→22.5 Å / Num. obs: 18228 / % possible obs: 94.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.227 / Net I/σ(I): 2.15
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 1830 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
CrysalisPro171.39.46data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IEP

3iep


Resolution: 3.1→17.86 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.858 / SU B: 39.298 / SU ML: 0.665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3326 924 5 %RANDOM
Rwork0.2772 ---
obs0.28 17435 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.92 Å2 / Biso mean: 36.955 Å2 / Biso min: 15.48 Å2
Baniso -1Baniso -2Baniso -3
1--3 Å20 Å21.7 Å2
2---9.93 Å2-0 Å2
3---11.95 Å2
Refinement stepCycle: final / Resolution: 3.1→17.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8426 0 84 0 8510
Biso mean--22.78 --
Num. residues----1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0158712
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178066
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.76111816
X-RAY DIFFRACTIONr_angle_other_deg0.7051.70318856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.17151080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69819.643280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.381540
X-RAY DIFFRACTIONr_chiral_restr0.0710.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219680
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021610
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 63 -
Rwork0.403 1328 -
all-1391 -
obs--96.87 %

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