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- PDB-8ubh: Solution NMR structure of KaiB variant from Thermosynechococcus e... -

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Basic information

Entry
Database: PDB / ID: 8ubh
TitleSolution NMR structure of KaiB variant from Thermosynechococcus elongatus vestitus (KaiBTV-4)
ComponentsCircadian oscillation regulator
KeywordsSIGNALING PROTEIN / Protein folding / metamorphic protein / Fold-switching
Function / homologyCircadian clock protein KaiB-like / KaiB domain / KaiB domain / KaiB / rhythmic process / Thioredoxin-like superfamily / Circadian oscillation regulator
Function and homology information
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsOjoawo, A. / Wayment-Steele, H.K. / Kern, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2024
Title: Predicting multiple conformations via sequence clustering and AlphaFold2.
Authors: Wayment-Steele, H.K. / Ojoawo, A. / Otten, R. / Apitz, J.M. / Pitsawong, W. / Homberger, M. / Ovchinnikov, S. / Colwell, L. / Kern, D.
History
DepositionSep 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / struct_keywords
Item: _audit_author.name / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 2.0Nov 29, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_contact_author ...atom_site / pdbx_contact_author / pdbx_nmr_ensemble / pdbx_struct_sheet_hbond / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis / struct_sheet_range
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_comp_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_comp_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_comp_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model orientation/position / Details: Replaced model to fixed Cis-peptides / Provider: author / Type: Coordinate replacement
Revision 2.1Dec 20, 2023Group: 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 / _citation_author.identifier_ORCID
Revision 2.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 2.3May 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: Circadian oscillation regulator


Theoretical massNumber of molelcules
Total (without water)9,9211
Polymers9,9211
Non-polymers00
Water0
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Circadian oscillation regulator


Mass: 9920.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: NIES-2133 / IAM M-273 / BP-1 / Gene: tll0553 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DLE2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aliphatic
121isotropic42D 1H-13C HSQC aromatic
131isotropic13D CBCA(CO)NH
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic12D 1H-15N HSQC
1101isotropic43D 1H-13C NOESY aliphatic
191isotropic43D 1H-13C NOESY aromatic
181isotropic33D C(CO)NH
171isotropic43D HBHA(CO)NH
1111isotropic33D H(CCO)NH
1121isotropic43D (H)CCH-TOCSY
1131isotropic43D 1H-15N NOESY
1141isotropic42D (HB)CB(CGCDCE)HDH AROMATIC
1151isotropic42D (HB)CB(CGCD)HD AROMATIC

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Sample preparation

DetailsType: solution
Contents: 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP, 90% H2O/10% D2O
Label: 15N, 13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMMOPSnatural abundance1
50 mMsodium chloridenatural abundance1
2 mMTCEPnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: Conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD7501
Bruker AVANCE NEOBrukerAVANCE NEO8002
Bruker AVANCE III HDBrukerAVANCE III HD6003
Varian Uniform NMR SystemVarianUniform NMR System8004

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Processing

NMR software
NameDeveloperClassification
PokyManthey, I. et al. POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data. J Struct Biol X 6, 100073 (2022). https://doi.org:10.1016/j.yjsbx.2022.100073chemical shift assignment
PINE ServerLee, W. et al. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR 73, 213-222 (2019). https://doi.org:10.1007/s10858-019-00255-3chemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PONDEROSA-C/SLee, W., Stark, J. L. & Markley, J. L. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J Biomol NMR 60, 73-75 (2014). https://doi.org:10.1007/s10858-014-9855-xstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
AUDANALee, W., Petit, C. M., Cornilescu, G., Stark, J. L. & Markley, J. L. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR 65, 51-57 (2016). https://doi.org:10.1007/s10858-016-0036-ystructure calculation
TALOS-NShen, Y. & Bax, A. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. Methods Mol Biol 1260, 17-32 (2015). https://doi.org:10.1007/978-1-4939-2239-0_2structure calculation
RefinementMethod: simulated annealing / Software ordinal: 9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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