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- PDB-6h7q: Trpzip2 structure in presence of exogenous haloprotectant molecule. -

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Basic information

Entry
Database: PDB / ID: 6h7q
TitleTrpzip2 structure in presence of exogenous haloprotectant molecule.
ComponentsTrpzip2
KeywordsANTIFREEZE PROTEIN / Stabilisation / Halophilic
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsPrior, S.H.
CitationJournal: To Be Published
Title: Trpzip2 structure in presence of exogenous haloprotectant molecule.
Authors: Prior, S.H.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2Nov 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: Trpzip2


Theoretical massNumber of molelcules
Total (without water)1,6091
Polymers1,6091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120 Å2
ΔGint1 kcal/mol
Surface area1490 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Trpzip2


Mass: 1608.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 2 mM Trpzip2, 50 mM potassium phosphate, 250 mM ectoine, 90% H2O/10% D2O
Label: na / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMTrpzip2natural abundance1
50 mMpotassium phosphatenatural abundance1
250 mMectoinenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: c1 / pH: 5.5 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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