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Entry
Database: PDB / ID: 2p6j
TitleFull-sequence computational design and solution structure of a thermostable protein variant
Componentsdesigned engrailed homeodomain variant UVF
KeywordsDE NOVO PROTEIN / HELIX-TURN-HELIX / COMPUTATIONAL PROTEIN DESIGN / ENGRAILED HOMEODOMAIN
Function / homologyHelix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesunidentified (others)
MethodSOLUTION NMR / simulated annealing, distance geometry
AuthorsShah, P.S. / Hom, G.K. / Ross, S.A. / Lassila, J.K. / Crowhurst, K.A. / Mayo, S.L.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Full-sequence Computational Design and Solution Structure of a Thermostable Protein Variant.
Authors: Shah, P.S. / Hom, G.K. / Ross, S.A. / Lassila, J.K. / Crowhurst, K.A. / Mayo, S.L.
History
DepositionMar 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999sequence Full sequence was computationally designed. The sequence is not availabe in UniProt ...sequence Full sequence was computationally designed. The sequence is not availabe in UniProt database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed engrailed homeodomain variant UVF


Theoretical massNumber of molelcules
Total (without water)6,6051
Polymers6,6051
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)43 / 100structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein designed engrailed homeodomain variant UVF


Mass: 6605.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111aliphatic 3D 13C-separated NOESY
121aromatic 3D 13C-separated NOESY
1313D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Hydrogen bond restraints were derived from protection factors measured by H/D exchange. Torsion angle restraints were ...Text: The structure was determined using triple-resonance NMR spectroscopy. Hydrogen bond restraints were derived from protection factors measured by H/D exchange. Torsion angle restraints were derived from J-coupling data (HNHA experiment) and from TALOS predictions.

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Sample preparation

Details
Solution-IDContentsSolvent system
1Uniform (random) labeling with 13C, 15N: U-13C, U-15N, 95% H2O, 5% D2O95% H2O/5% D2O
2Uniform (random) labeling with 15N: U-15N, 95% H2O, 5% D2O95% H2O/5% D2O
3Uniform (random) labeling with 13C, 15N: U-13C, U-15N, 100% D2O100% D2O
Sample conditionsIonic strength: 50 mM sodium phosphate / pH: 5.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Cvariancollection
NMRPipeDelaglio, F. et al.processing
NMRView4Johnson, B.A. et al.data analysis
ARIA1.2Nilges, M. et al.refinement
ARIA1.2Nilges, M. et al.structure solution
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
Details: The structures are based on a total of 1321 restraints: 1245 are NOE-derived distance constraints, 57 are dihedral angle restraints and 19 distance restraints are from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 43

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