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- PDB-2rvd: NMR STRUCTURE of A MUTANT OF CHIGNOLIN, CLN025 -

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Basic information

Entry
Database: PDB / ID: 2rvd
TitleNMR STRUCTURE of A MUTANT OF CHIGNOLIN, CLN025
ComponentsCLN025
KeywordsDE NOVO PROTEIN / BETA-HAIRPIN / MINI-PROTEIN / CHIGNOLIN
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsKato, Y. / Ishimura, M. / Honda, S.
Citation
#2: Journal: Structure / Year: 2004
Title: 10 Residue folded peptide designed by segment statistics
Authors: Honda, S. / Yamasaki, K. / Sawada, Y. / Morii, H.
History
DepositionJul 14, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLN025


Theoretical massNumber of molelcules
Total (without water)1,2941
Polymers1,2941
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CLN025


Mass: 1294.322 Da / Num. of mol.: 1 / Mutation: G1Y/G10Y / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H ROESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsSolvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMCLN025-1natural abundance1
20 mMsodium phosphate-2natural abundance1
0.02 %sodium azide-3natural abundance1
0.01 %DSS-4natural abundance1
95 %H2O-5natural abundance1
5 %D2O-6natural abundance1
Sample conditionspH: 5.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
VNMRVariancollection
CYANArefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 80 / NOE intraresidue total count: 26 / NOE long range total count: 15 / NOE medium range total count: 22 / NOE sequential total count: 17
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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