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- PDB-6k4d: Ancestral luciferase AncLamp in complex with ATP and D-luciferin -

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Basic information

Entry
Database: PDB / ID: 6k4d
TitleAncestral luciferase AncLamp in complex with ATP and D-luciferin
ComponentsAncestral luciferase AncLamp
KeywordsOXIDOREDUCTASE / Luciferase / Bioluminescence / Ancestral protein / Molecular evolution
Function / homologyChem-D4F / Chem-ESJ
Function and homology information
Biological speciesLampyridae (fireflies)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOba, Y. / Konishi, K. / Yano, D. / Kato, D. / Shirai, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)17am0101111j0001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H01818 Japan
CitationJournal: Sci Adv / Year: 2020
Title: Resurrecting the ancient glow of the fireflies.
Authors: Oba, Y. / Konishi, K. / Yano, D. / Shibata, H. / Kato, D. / Shirai, T.
History
DepositionMay 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 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
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: Ancestral luciferase AncLamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2643
Polymers60,3741
Non-polymers8902
Water13,151730
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21930 Å2
Unit cell
Length a, b, c (Å)48.760, 123.680, 177.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1186-

HOH

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Components

#1: Protein Ancestral luciferase AncLamp


Mass: 60374.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lampyridae (fireflies) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-D4F / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (4S)-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate / Luciferyl adenylate


Mass: 609.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H20N7O9PS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ESJ / (4S)-2-(6-hydroxy-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid / D-LUCIFERIN


Mass: 280.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H8N2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M trisodium citrate buffer (pH 5.5), 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 55829 / % possible obs: 96.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.014 / Net I/σ(I): 75.6
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.03 / Num. unique obs: 2520

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d1r

2d1r


Resolution: 1.7→19.888 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 2833 5.07 %
Rwork0.1561 --
obs0.1578 55829 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 58 730 4986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084398
X-RAY DIFFRACTIONf_angle_d0.9435964
X-RAY DIFFRACTIONf_dihedral_angle_d13.9561637
X-RAY DIFFRACTIONf_chiral_restr0.063669
X-RAY DIFFRACTIONf_plane_restr0.006764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.27751250.21882520X-RAY DIFFRACTION90
1.7293-1.76070.25651430.21772440X-RAY DIFFRACTION89
1.7607-1.79460.23241530.20362519X-RAY DIFFRACTION90
1.7946-1.83120.24871500.19142500X-RAY DIFFRACTION91
1.8312-1.8710.24051250.18552568X-RAY DIFFRACTION91
1.871-1.91450.23091390.18282539X-RAY DIFFRACTION91
1.9145-1.96230.21311470.17312561X-RAY DIFFRACTION91
1.9623-2.01530.18431340.1672552X-RAY DIFFRACTION91
2.0153-2.07450.24971240.15852591X-RAY DIFFRACTION93
2.0745-2.14140.20311530.15812567X-RAY DIFFRACTION92
2.1414-2.21790.1821380.15462621X-RAY DIFFRACTION93
2.2179-2.30650.2131340.16232596X-RAY DIFFRACTION94
2.3065-2.41130.17321390.16192639X-RAY DIFFRACTION94
2.4113-2.53820.18981190.16182757X-RAY DIFFRACTION97
2.5382-2.69690.21051560.16362728X-RAY DIFFRACTION97
2.6969-2.90450.18311510.16072761X-RAY DIFFRACTION98
2.9045-3.19580.19541450.15322815X-RAY DIFFRACTION99
3.1958-3.65570.15541460.14072832X-RAY DIFFRACTION99
3.6557-4.59640.14331650.12292876X-RAY DIFFRACTION100
4.5964-19.88890.1631470.14173014X-RAY DIFFRACTION100

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