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- PDB-2nd2: Solution structure of the de novo mini protein gHHH_06 -

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Basic information

Entry
Database: PDB / ID: 2nd2
TitleSolution structure of the de novo mini protein gHHH_06
ComponentsDe novo mini protein HHH_06
KeywordsDE NOVO PROTEIN / engineered protein
Biological speciesartificial gene (others)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsPulavarti, S.V. / Eletsky, A. / Bahl, C.D. / Buchko, G.W. / Baker, D. / Szyperski, T.
CitationJournal: Nature / Year: 2016
Title: Accurate de novo design of hyperstable constrained peptides.
Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P. ...Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P.J. / Rocklin, G.J. / Song, Y. / Linsky, T.W. / Watkins, A. / Rettie, S.A. / Xu, X. / Carter, L.P. / Bonneau, R. / Olson, J.M. / Coutsias, E. / Correnti, C.E. / Szyperski, T. / Craik, D.J. / Baker, D.
History
DepositionApr 22, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo mini protein HHH_06


Theoretical massNumber of molelcules
Total (without water)5,1301
Polymers5,1301
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide De novo mini protein HHH_06


Mass: 5129.892 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (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
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1412D 1H-1H DPFGSE TOCSY
1512D 1H-1H DPFGSE NOESY
1613D HNCO
1713D HNCA
1813D 1H-15N NOESY HSQC
1913D 1H-15N TOCSY HSQC
11013D HNHA
11113D HNHB

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 4 uM DSS, 0.02 % sodium azide, 1 mM [U-100% 15N] HHH_06, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
4 uMDSS-21
10 %D2O-3[U-99% 2H]1
0.02 %sodium azide-41
1 mMHHH_06-5[U-100% 15N]1
Sample conditionsIonic strength: 50 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DD2AgilentDD26001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
PROSAGuntertprocessing
XEASYBartels et al.data analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
PdbStatpdbstat (Moseley, Montelione)data analysis
PSVSBhattacharya and Montelionevalidation
PSVSBhattacharya and Montelionerpf calculation
PSVSBhattacharya and Montelioneviolations
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 780 / NOE intraresidue total count: 228 / NOE long range total count: 62 / NOE medium range total count: 266 / NOE sequential total count: 224 / Protein phi angle constraints total count: 27 / Protein psi angle constraints total count: 27
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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