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- PDB-2gjf: NMR structure of the computationally designed procarboxypeptidase... -

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Basic information

Entry
Database: PDB / ID: 2gjf
TitleNMR structure of the computationally designed procarboxypeptidase-A (1AYE) domain
ComponentsDESIGNED PROTEIN
KeywordsDE NOVO PROTEIN / designed protein / procarboxypeptidase
Function / homologyMetallocarboxypeptidase-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsReichow, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design.
Authors: Dantas, G. / Corrent, C. / Reichow, S.L. / Havranek, J.J. / Eletr, Z.M. / Isern, N.G. / Kuhlman, B. / Varani, G. / Merritt, E.A. / Baker, D.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The protein has been computationally designed based on human procarboxypeptidase-A (1AYE) ...SEQUENCE The protein has been computationally designed based on human procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability. A six residue HIS tag is present at the N-terminus.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DESIGNED PROTEIN
B: DESIGNED PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,0222
Polymers18,0222
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein DESIGNED PROTEIN


Mass: 9011.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Plasmid: pET 29(b) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3)

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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 AYE, 50mM phosphate buffer, pH 7.0, 100mM KCl, 90% H2O, 10% D2O90% H2O/10% D2O
21mM AYE, 50mM phosphate buffer, pH 7.0, 100mM KCl, 100% D2O100% D2O
31mM AYE U-15N, 13C, 50mM phosphate buffer, pH 7.0, 100mM KCl, 90% H2O, 10% D2O90% H2O/10% D2O
41mM AYE U-15N, 50mM phosphate buffer, pH 7.0, 100mM KCl, 90% H2O, 10% D2O90% H2O/10% D2O
51.4mM AYE U-15N, 13C, 1.4mM 14N,12C AYE, 50mM phosphate buffer, pH 7.0, 100mM KCl,100% D2O100% D2O
Sample conditionsIonic strength: 150mM / 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
CYANA2.1P.Guntert et al.refinement
CYANA2.1P.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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