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- PDB-7dab: plant peptide hormone -

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Basic information

Entry
Database: PDB / ID: 7dab
Titleplant peptide hormone
ComponentsMaternally expressed gene14
KeywordsPLANT PROTEIN / STRUCTURE FROM CYANA 2.1 / UNKNOWN FUNCTION
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Maternally expressed gene14
Function and homology information
Biological speciesZea mays (maize)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsUmetsu, Y. / Ohki, S.
CitationJournal: To Be Published
Title: plant peptide hormone
Authors: Ohki, S. / Mori, M.
History
DepositionOct 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Maternally expressed gene14


Theoretical massNumber of molelcules
Total (without water)6,8811
Polymers6,8811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5400 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Maternally expressed gene14 / Maternally expressed protein 14


Mass: 6880.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: Meg14, ZEAMMB73_Zm00001d019033 / Production host: Nicotiana tabacum (common tobacco) / References: UniProt: A0A076YHT9
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
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-15N TOCSY
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

DetailsType: solution
Contents: 0.2 mM 13C, 15N protein, 50 mM unlabeled potassium phosphate, 50 mM unlabeled potassium chloride, 90% H2O/10% D2O
Details: 0.2mM protein 50mM phosphate buffer (pH6.8) 50mM KCl
Label: 13C, 15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMprotein13C, 15N1
50 mMpotassium phosphateunlabeled1
50 mMpotassium chlorideunlabeled1
Sample conditionsDetails: uniformly labeled / Ionic strength: 100 mM / Label: 13C, 15N / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
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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