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- PDB-7bqq: Solution NMR structure of fold-Z Gogy; de novo designed protein w... -

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Basic information

Entry
Database: PDB / ID: 7bqq
TitleSolution NMR structure of fold-Z Gogy; de novo designed protein with an asymmetric all-alpha topology
ComponentsGogy
KeywordsDE NOVO PROTEIN / de novo designed protein
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsKobayashi, N. / Sugiki, T. / Fujiwara, T. / Sakuma, K. / Kosugi, T. / Koga, R. / Koga, N.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06152 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101072 Japan
Japan Society for the Promotion of Science (JSPS)18H05420 Japan
Japan Society for the Promotion of Science (JSPS)15H05592 Japan
Japan Science and TechnologyJPMJPR13AD Japan
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Design of complicated all-alpha protein structures
Authors: Sakuma, K. / Kobayashi, N. / Sugiki, T. / Nagashima, T. / Fujiwara, T. / Suzuki, K. / Kobayashi, N. / Murata, T. / Kosugi, T. / Koga, R. / Koga, N.
History
DepositionMar 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2Jan 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 15, 2024Group: Database references / Category: 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: Gogy


Theoretical massNumber of molelcules
Total (without water)15,2961
Polymers15,2961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8180 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Gogy


Mass: 15296.273 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
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D BEST-HNCO
151isotropic23D BEST-HN(CA)CB
181isotropic13D (H)CCH-TOCSY aliphatic
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic
191isotropic23D 1H-13C NOESY aromatic
1101isotropic32D 1H-15N HSQC IPAP
1112anisotropic32D 1H-15N HSQC IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.9 mM [U-100% 13C; U-100% 15N] Gogy, 6.8 mM potassium phosphate, 3.20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2OGogy95% H2O/5% D2O
solution20.2 mM [U-100% 13C; U-100% 15N] Gogy, 6.8 mM potassium phosphate, 3.2 mM sodium phosphate, 50 mM sodium chloride, 7 mg/mL Pf1 phage, 95% H2O/5% D2OGogy_phage95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMGogy[U-100% 13C; U-100% 15N]1
6.8 mMpotassium phosphatenatural abundance1
3.20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.2 mMGogy[U-100% 13C; U-100% 15N]2
6.8 mMpotassium phosphatenatural abundance2
3.2 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
7 mg/mLPf1 phagenatural abundance2
Sample conditionsIonic strength: 60 mM / Label: Gogy / pH: 6.52 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III9503

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipe2017Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MAGRO2.01.14Updated version of Kujira (Kobayashi, N. et al., 2007)peak picking
NMRView9Johnson, One Moon Scientificdata analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichchemical shift assignment
TALOS2017Cornilescu, Delaglio and Baxdata analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 8
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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