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- PDB-6dmp: De Novo Design of a Protein Heterodimer with Specificity Mediated... -

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Basic information

Entry
Database: PDB / ID: 6dmp
TitleDe Novo Design of a Protein Heterodimer with Specificity Mediated by Hydrogen Bond Networks
Components
  • Designed orthogonal protein DHD13_XAAA_A
  • Designed orthogonal protein DHD13_XAAA_B
KeywordsDE NOVO PROTEIN / Computational design / coiled coil
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, Z. / Flores-Solis, D. / Sgourakis, N.G. / Baker, D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIAID(AI2573-01) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM125034-01 United States
National Institutes of Health/Office of the DirectorHIE-S10OD018455 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2019
Title: Programmable design of orthogonal protein heterodimers.
Authors: Chen, Z. / Boyken, S.E. / Jia, M. / Busch, F. / Flores-Solis, D. / Bick, M.J. / Lu, P. / VanAernum, Z.L. / Sahasrabuddhe, A. / Langan, R.A. / Bermeo, S. / Brunette, T.J. / Mulligan, V.K. / ...Authors: Chen, Z. / Boyken, S.E. / Jia, M. / Busch, F. / Flores-Solis, D. / Bick, M.J. / Lu, P. / VanAernum, Z.L. / Sahasrabuddhe, A. / Langan, R.A. / Bermeo, S. / Brunette, T.J. / Mulligan, V.K. / Carter, L.P. / DiMaio, F. / Sgourakis, N.G. / Wysocki, V.H. / Baker, D.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed orthogonal protein DHD13_XAAA_A
B: Designed orthogonal protein DHD13_XAAA_B


Theoretical massNumber of molelcules
Total (without water)19,1432
Polymers19,1432
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration: Protein is monodisperse and eluted at the expected volume corresponding to a heterodimer assembly
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3250 Å2
ΔGint-29 kcal/mol
Surface area9840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Designed orthogonal protein DHD13_XAAA_A


Mass: 9344.792 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)
#2: Protein Designed orthogonal protein DHD13_XAAA_B


Mass: 9798.264 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)

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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
131isotropic14D HNCH TOCSY
141isotropic14D HNCH NOESY
151isotropic14D (H)CCH NOESY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] DHD13_XAAA, 1.0 mM [U-13C; U-15N] DHD13_XAAB. 90% H2O/10% D2O
Label: 13C_15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMDHD13_XAAA[U-13C; U-15N]1
1.0 mMDHD13_XAAB[U-13C; U-15N]1
Sample conditionsDetails: 50 mM NaCl 20 mM NaPO4 / Ionic strength: 0.1 M / Ionic strength err: 0.02 / Label: NMR_buffer_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz / Details: CRYOPROBE

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Processing

NMR software
NameVersionDeveloperClassification
CS-ROSETTA3Shen, Vernon, Baker and Baxrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CS-ROSETTA3Shen, Vernon, Baker and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 10000 / Conformers submitted total number: 10

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