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- PDB-2gjh: NMR Structure of CFr (C-terminal fragment of computationally desi... -

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Basic information

Entry
Database: PDB / ID: 2gjh
TitleNMR Structure of CFr (C-terminal fragment of computationally designed novel-topology protein Top7)
ComponentsDESIGNED PROTEINDesign
KeywordsDE NOVO PROTEIN / Obligate symmetric homo-dimer
Function / homologyCell Cycle; Chain A - #20 / Cell Cycle; Chain A / 2-Layer Sandwich / Alpha Beta
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDantas, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution.
Authors: Dantas, G. / Watters, A.L. / Lunde, B.M. / Eletr, Z.M. / Isern, N.G. / Roseman, T. / Lipfert, J. / Doniach, S. / Tompa, M. / Kuhlman, B. / Stoddard, B.L. / Varani, G. / Baker, D.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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
Remark 999SEQUENCE The protein has been computationally designed. Residues 1, 2, 52-62 were added to the ...SEQUENCE The protein has been computationally designed. Residues 1, 2, 52-62 were added to the original protein construct to allow for expression and purification, including a C-terminal six residue HIS tag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DESIGNED PROTEIN
B: DESIGNED PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,1002
Polymers14,1002
Non-polymers00
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein DESIGNED PROTEIN / Design


Mass: 7049.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Plasmid: pET 29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLYSS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1333D 13C-separated NOESY
1443D 15N-separated NOESY
1553D 13C-filtered NOESY
NMR detailsText: Hydrogen bond restraints were derived from D2O protection analysis. Torsion angle restraints were derived from TALOS predictions

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM CFr, 25mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
21mM CFr, 25mM phosphate buffer, pH 7.0, 100% D2O100% D2O
31.0mM CFr U-15N, 13C, 25mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
41.0mM CFr U-15N, 25mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
51.4mM CFr U-15N, 13C, 1.4mM 14N, 12C CFr, 25mM phosphate buffer, pH 7.0, 100% D2O100% D2O
Sample conditionsIonic strength: 25mM / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DRXBrukerDRX5002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2P.Guntert et al.refinement
CYANA2P.Guntert et al.structure solution
TALOSG. Cornilescu et al.data analysis
NMRPipe2.3F. Delaglio et al.processing
Sparky3.112T. Goddard and D. Knellerdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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