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- PDB-5tx8: Solution structure of the de novo mini protein gHH_44 -

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Basic information

Entry
Database: PDB / ID: 5tx8
TitleSolution structure of the de novo mini protein gHH_44
ComponentsHH2
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Bahl, C.D. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
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
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: 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 1.3Jan 15, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_nmr_software.name
Revision 1.4Jun 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 1.5Nov 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: HH2


Theoretical massNumber of molelcules
Total (without water)3,3671
Polymers3,3671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide HH2


Mass: 3366.862 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (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-IDSample stateSpectrometer-IDType
111anisotropic13D C(CO)NH
121anisotropic33D 1H-15N NOESY
131anisotropic23D 1H-13C NOESY aliphatic
141anisotropic23D HNCA
151anisotropic22D 1H-13C HSQC aliphatic
161anisotropic12D 1H-15N HSQC
172anisotropic2D20 exchange

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 13C; U-99% 15N] HH2, 25 mM sodium acetate, 50 mM sodium chloride, 93% H2O/7% D2OHH293% H2O/7% D2O
solution21 mM [U-99% 13C; U-99% 15N] HH2, 25 mM sodium acetate, 50 mM sodium chloride, 100% D2OHH2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHH2[U-99% 13C; U-99% 15N]1
25 mMsodium acetatenone1
50 mMsodium chloridenone1
1 mMHH2[U-99% 13C; U-99% 15N]2
25 mMsodium acetatenone2
50 mMsodium chloridenone2
Sample conditionsIonic strength: 0.075 M / Ionic strength err: 0.005 / Label: HH2 / pH: 4.8 Not defined / PH err: 0.2 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS6001
Varian VXRSVarianVXRS8002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. et.al.refinement
Sparky3.115Goddarddata analysis
Felix2007Accelrys Software Inc.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
PSVS1.5Bhattacharya and Montelionechemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 5
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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