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- PDB-2cw1: Solution structure of the de novo-designed lambda Cro fold protein -

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Basic information

Entry
Database: PDB / ID: 2cw1
TitleSolution structure of the de novo-designed lambda Cro fold protein
ComponentsSN4m
KeywordsDE NOVO PROTEIN / LAMBDA CRO FOLD
Function / homologyCRO Repressor / CRO Repressor / 2-Layer Sandwich / Alpha Beta
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsIsogai, Y. / Ito, Y. / Ikeya, T. / Shiro, Y. / Ota, M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein.
Authors: Isogai, Y. / Ito, Y. / Ikeya, T. / Shiro, Y. / Ota, M.
History
DepositionJun 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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 1.4May 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: SN4m


Theoretical massNumber of molelcules
Total (without water)7,4891
Polymers7,4891
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)10 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SN4m


Mass: 7488.702 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.8mM SN4m U-15N,13C; 10mM sodium phosphate buffer (pH 7.0) containing 200mM NaCl; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 200mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 303 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
XwinNMR2.6Brukercollection
Azara2.7Boucherprocessing
ANSIG3.3Kraulisdata analysis
CNS1.1Brungerstructure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 10

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