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- PDB-2e4e: NMR structure of D4P/K7G mutant of GPM12 -

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Basic information

Entry
Database: PDB / ID: 2e4e
TitleNMR structure of D4P/K7G mutant of GPM12
ComponentsGPM12
KeywordsDE NOVO PROTEIN / beta-hairpin / mini-protein / chignolin / B1 domain of protein G
MethodSOLUTION NMR / simulated annealing
AuthorsTerada, T. / Satoh, D. / Mikawa, T. / Ito, Y. / Shimizu, K.
CitationJournal: To be Published
Title: Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation
Authors: Terada, T. / Satoh, D. / Mikawa, T. / Ito, Y. / Shimizu, K.
History
DepositionDec 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GPM12


Theoretical massNumber of molelcules
Total (without water)9851
Polymers9851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide GPM12 / chignolin


Mass: 985.006 Da / Num. of mol.: 1 / Mutation: D4P, K7G / Source method: obtained synthetically / Details: CHEMICAL PEPTIDE SYNTHESIS
Sequence detailsTHERE ARE MUTANTS D4P, K7G. THESE MUTATIONS CONVERT THE DISORDERD STRUCTURE OF GPM12 INTO A ...THERE ARE MUTANTS D4P, K7G. THESE MUTATIONS CONVERT THE DISORDERD STRUCTURE OF GPM12 INTO A CHIGNOLIN-LIKE ORDERED STRUCTURE. SEQUENCE OF RESIDUES 2-9 OF GPM12 IS THE SAME AS THAT OF RESIDUES 45-52 OF THE B1 DOMAIN OF PROTEIN G.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D ROESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM GPM12(D4P/K7G) / Solvent system: 20mM sodium phosphate buffer
Sample conditionspH: 5.5 / Pressure: 1 atm / Temperature: 277 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker BioSpin Corporationcollection
Azara2.7Wayne Boucherprocessing
ANSIG3.3 for OpenGL version 1.0.6Per Kraulis, Takeshi Nishimuradata analysis
CNS1.1Axel T.Brunger et al.structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 119 NOE-derived distance constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 23

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