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- PDB-2nc6: Solution Structure of N-L-idosylated Pin1 WW Domain -

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Basic information

Entry
Database: PDB / ID: 2nc6
TitleSolution Structure of N-L-idosylated Pin1 WW Domain
ComponentsPin1 WW Domain
KeywordsISOMERASE / enhanced aromatic sequon
Function / homologybeta-L-idopyranose
Function and homology information
Biological specieshomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model20
AuthorsHsu, C. / Park, S. / Mortenson, D.E. / Foley, B. / Wang, X. / Woods, R.J. / Case, D.A. / Powers, E.T. / Wong, C. / Dyson, H. / Kelly, J.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate.
Authors: Hsu, C.H. / Park, S. / Mortenson, D.E. / Foley, B.L. / Wang, X. / Woods, R.J. / Case, D.A. / Powers, E.T. / Wong, C.H. / Dyson, H.J. / Kelly, J.W.
History
DepositionMar 20, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Mar 20, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / struct_conn
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_nmr_software / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_nmr_software.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 14, 2023Group: Database references / Other / Structure summary / Category: chem_comp / database_2 / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pin1 WW Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0292
Polymers3,8491
Non-polymers1801
Water0
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 Pin1 WW Domain


Mass: 3849.313 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (synth.) homo sapiens (human)
#2: Sugar ChemComp-4N2 / beta-L-idopyranose / beta-L-idose / L-idose / idose / Idose


Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LIdopbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-idopyranoseCOMMON NAMEGMML 1.0
b-L-IdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
IdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.5 uM Pin WW Domain Peptide, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 uM / Component: Pin WW Domain Peptide-1
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 285 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
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
Amberrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 516 / NOE intraresidue total count: 292 / NOE long range total count: 83 / NOE medium range total count: 38 / NOE sequential total count: 103 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 29 / Protein psi angle constraints total count: 29
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.24 Å
NMR ensemble rmsDistance rms dev: 0.235 Å

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