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- PDB-5w9f: Solution structure of the de novo mini protein gHEEE_02 -

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Basic information

Entry
Database: PDB / ID: 5w9f
TitleSolution structure of the de novo mini protein gHEEE_02
ComponentsDe novo mini protein gHEEE_02
KeywordsDE NOVO PROTEIN / De-novo design
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsPulavarti, S.V.S.R.K. / Shaw, E.A. / Bahl, C.D. / Garry, B.W. / Baker, D. / Szyperski, T.
CitationJournal: Protein Sci. / Year: 2018
Title: Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides.
Authors: Buchko, G.W. / Pulavarti, S.V.S.R.K. / Ovchinnikov, V. / Shaw, E.A. / Rettie, S.A. / Myler, P.J. / Karplus, M. / Szyperski, T. / Baker, D. / Bahl, C.D.
History
DepositionJun 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: De novo mini protein gHEEE_02


Theoretical massNumber of molelcules
Total (without water)4,9011
Polymers4,9011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3120 Å2
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 gHEEE_02


Mass: 4900.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pCDB367 / 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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D CBCA(CO)NH
1101isotropic13D HN(CA)CB
191isotropic13D HBHA(CO)NH
181isotropic13D (H)CCH-TOCSY
171isotropic1GFT 4,3D (H)CCH-COSY
161isotropic13D 15N/13Caliphatic/13Caromatic-edited [1H,1H]-NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C;15N] gHEEE_02, 5 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O
Details: 50 mM sodium phosphate, 5 uM DSS, 0.02 % sodium azide, 1 mM [U-13C;15N] gHEEE_02, 90% H2O/10% D2O
Label: gHEEE_02_NC / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMgHEEE_02[U-13C;15N]1
5 uMDSSnatural abundance1
10 %d20natural abundance1
0.02 %sodium azidenatural abundance1
Sample conditionsIonic strength: 50 mM / Ionic strength err: 0.1 / Label: 1 / pH: 6.0 / PH err: 0.1 / Pressure: ambient / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz
Details: High field NMR facility, Dept. of Chemistry, SUNY Buffalo

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
PROSA6.4Guntertprocessing
XEASYBartels et al.data analysis
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichchemical shift calculation
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.5Bhattacharya and Montelionedata analysis
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: torsion angle dynamics with CYANA
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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