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- PDB-8x0r: solution structure of Cry j 7 -

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Basic information

Entry
Database: PDB / ID: 8x0r
Titlesolution structure of Cry j 7
ComponentsCypmaclein
KeywordsSTRUCTURAL PROTEIN / STRUCTURE FROM CYANA 2.1
Function / homologyGibberellin regulated protein / Gibberellin regulated protein / Cypmaclein
Function and homology information
Biological speciesCryptomeria japonica (Japanese cedar)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsZheng, J. / Aizawa, T. / Kumeta, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCE1301 Japan
Japan Science and TechnologyJPMJPF2108 Japan
Japan Science and TechnologyJPMJSP2119 Japan
CitationJournal: To Be Published
Title: solution structure of Cry j 7
Authors: Zheng, J. / Aizawa, T. / Kumeta, H.
History
DepositionNov 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cypmaclein


Theoretical massNumber of molelcules
Total (without water)6,9131
Polymers6,9131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Cypmaclein


Mass: 6912.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptomeria japonica (Japanese cedar) / Production host: Komagataella pastoris (fungus) / References: UniProt: C0HLQ1
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-1H NOESY
141isotropic12D 1H-1H TOCSY
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-15N TOCSY
171isotropic13D HNCO
181isotropic13D HNCA

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-99% 15N] Cry j 7, 10 % v/v [U-99% 2H] D2O, 90% H2O/10% D2O
Label: N_Cry j 7 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMCry j 7[U-99% 15N]1
10 % v/vD2O[U-99% 2H]1
Sample conditionsIonic strength: 0 M / Label: conditions_1 / pH: 3 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.1Bruker Biospincollection
VNMR6.1CVariancollection
NMRPipe9.6Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
TALOS+9.6Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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