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- PDB-7d2o: Solution structure of Gaussia Luciferase by NMR -

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Basic information

Entry
Database: PDB / ID: 7d2o
TitleSolution structure of Gaussia Luciferase by NMR
ComponentsLuciferase
KeywordsLUMINESCENT PROTEIN / Luciferase
Function / homologyLuciferase
Function and homology information
Biological speciesGaussia princeps (T. Scott
1894)
MethodSOLUTION NMR / simulated annealing
AuthorsKobayashi, N. / Wu, N. / Kuroda, Y. / Yamazaki, T.
CitationJournal: Sci Rep / Year: 2020
Title: Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR.
Authors: Wu, N. / Kobayashi, N. / Tsuda, K. / Unzai, S. / Saotome, T. / Kuroda, Y. / Yamazaki, T.
History
DepositionSep 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Luciferase


Theoretical massNumber of molelcules
Total (without water)18,8521
Polymers18,8521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Luciferase / GLuc


Mass: 18851.838 Da / Num. of mol.: 1 / Mutation: E117A, G120R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gaussia princeps (T. Scott, 1894) / Strain: T. Scott, 1894 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BLZ2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CB
161isotropic13D HN(CO)CA
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-13C; U-15N] Gluc, 50 mM MES, 2 mM sodium azide, 90% H2O/10% D2O
Label: Gluc / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMGluc[U-13C; U-15N]1
50 mMMESnatural abundance1
2 mMsodium azidenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: Gluc / pH: 6 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
MagRO-NMRView2.01.33Kobayashi, N.peak picking
MagRO-NMRView2.01.33Kobayashi, N.chemical shift assignment
NMRPipe2017Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3.98Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 19

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