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- PDB-2jre: C60-1, a PDZ domain designed using statistical coupling analysis -

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Basic information

Entry
Database: PDB / ID: 2jre
TitleC60-1, a PDZ domain designed using statistical coupling analysis
ComponentsC60-1 PDZ domain peptide
KeywordsDE NOVO PROTEIN / C60-1 / PDZ
Function / homologyPDZ domain / Pdz3 Domain / Roll / Mainly Beta
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsLarson, C. / Stiffler, M. / Li, P. / Rosen, M. / MacBeath, G. / Ranganathan, R.
CitationJournal: To be Published
Title: C60-1, a PDZ domain designed using statistical coupling analysis
Authors: Larson, C. / Stiffler, M. / Li, P. / Rosen, M. / MacBeath, G. / Ranganathan, R.
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C60-1 PDZ domain peptide


Theoretical massNumber of molelcules
Total (without water)11,5891
Polymers11,5891
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein C60-1 PDZ domain peptide


Mass: 11589.026 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide is a synthetic construct designed using statistical coupling analysis and expressed in Escherichia coli BL21 cells using the pHis8.3 vector.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1312D 1H-15N HSQC
1432D 1H-13C HSQC
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HNCO
1813D C(CO)NH
1913D H(CCO)NH
11023D (H)CCH-TOCSY
21112D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium chloride, 25 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium chloride, 25 mM sodium phosphate, 0.02 % sodium azide, 100% D2O100% D2O
31 mM [U-10% 13C] protein, 50 mM sodium chloride, 25 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity[U-100% 13C; U-100% 15N]1
50 mMsodium chloride1
25 mMsodium phosphate1
0.02 %sodium azide1
1 mMentity[U-100% 13C; U-100% 15N]2
50 mMsodium chloride2
25 mMsodium phosphate2
0.02 %sodium azide2
1 mMentity[U-10% 13C]3
50 mMsodium chloride3
25 mMsodium phosphate3
0.02 %sodium azide3
Sample conditionspH: 6.5 / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY6001
Varian UnityVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1718 / NOE intraresidue total count: 675 / NOE long range total count: 430 / NOE medium range total count: 152 / NOE sequential total count: 378 / Hydrogen bond constraints total count: 64 / Protein phi angle constraints total count: 51 / Protein psi angle constraints total count: 51
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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