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- PDB-8qnj: Folded alpha helical de novo proteins from Apilactobacillus kunkeei -

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Basic information

Entry
Database: PDB / ID: 8qnj
TitleFolded alpha helical de novo proteins from Apilactobacillus kunkeei
ComponentsLenovo Protein
KeywordsUNKNOWN FUNCTION / secreted protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesApilactobacillus kunkeei (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsCelestine, C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei.
Authors: Ye, W. / Krishna Behra, P.R. / Dyrhage, K. / Seeger, C. / Joiner, J.D. / Karlsson, E. / Andersson, E. / Chi, C.N. / Andersson, S.G.E. / Jemth, P.
History
DepositionSep 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 2.0Mar 27, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / entity_name_com ...atom_site / entity_name_com / entity_src_gen / pdbx_nmr_representative / pdbx_validate_torsion / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_gene_src_gene / _pdbx_nmr_representative.conformer_id / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1May 8, 2024Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lenovo Protein


Theoretical massNumber of molelcules
Total (without water)7,4371
Polymers7,4371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Lenovo Protein


Mass: 7437.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apilactobacillus kunkeei (bacteria) / Gene: FF306_00167 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L8CFV4

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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
131isotropic13D HN(CA)CB
141isotropic13D HN(COCA)CB
151isotropic13D 1H-13C NOESY
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-10% 13C; U-99% 15N] Orphan 5, 90% H2O/10% D2O
Label: 15N, 13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 500 uM / Component: Orphan 5 / Isotopic labeling: [U-10% 13C; U-99% 15N]
Sample conditionsIonic strength: 150 mM / Label: conditions / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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