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- PDB-2nd3: Solution structure of the de novo mini protein gEEH_04 -

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Basic information

Entry
Database: PDB / ID: 2nd3
TitleSolution structure of the de novo mini protein gEEH_04
ComponentsDe novo mini protein EEH_04
KeywordsDE NOVO PROTEIN / engineered protein
Biological speciesartificial gene (others)
MethodSOLUTION NMR / distance geometry, molecular dynamics
Model detailslowest energy, model1
AuthorsPulavarti, S.V. / Bahl, C.D. / Gilmore, J.M. / Eletsky, A. / 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: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo mini protein EEH_04


Theoretical massNumber of molelcules
Total (without water)4,6641
Polymers4,6641
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide De novo mini protein EEH_04


Mass: 4664.215 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)
Has protein modificationY

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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-13C HSQC aliphatic ct
1512D 1H-13C HSQC aliphatic ct
1612D 1H-1H DPFGSE TOCSY
1712D 1H-1H DPFGSE NOESY
1813D HNHA
1913D HNCO
11013D HNCA
11113D HNHB
11213D 1H-15N NOESY HSQC
11313D 1H-15N TOCSY HSQC

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Sample preparation

DetailsContents: 1 mM [U-10% 13C; U-100% 15N] EEH_04, 50 mM sodium phosphate, 4 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMEEH_04-1[U-10% 13C; U-100% 15N]1
50 mMsodium phosphate-21
4 uMDSS-31
10 %D2O-4[U-99% 2H]1
0.02 %sodium azide-51
Sample conditionsIonic strength: 50 / pH: 6 / 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
VNMRVariancollection
PROSAGuntertprocessing
XEASYBartels et al.data analysis
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdihedral angle prediction
PSVSBhattacharya and Montelioneassignment validation
PSVSBhattacharya and Montelionerpf calculation
PSVSBhattacharya and Montelioneviolations
RefinementMethod: distance geometry, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 614 / NOE intraresidue total count: 135 / NOE long range total count: 157 / NOE medium range total count: 156 / NOE sequential total count: 166
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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