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- PDB-7jh1: Solution structure of a reconstructed XCL1 ancestor -

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Basic information

Entry
Database: PDB / ID: 7jh1
TitleSolution structure of a reconstructed XCL1 ancestor
ComponentsXCL1 ancestor
KeywordsCYTOKINE / metamorphic protein / chemokine / ancestral reconstruction
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTyler, R.C. / Peterson, F.C. / Volkman, B.F.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI103225 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI058072 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 OD020000 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F30 CA236182 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM080202 United States
CitationJournal: Science / Year: 2021
Title: Evolution of fold switching in a metamorphic protein.
Authors: Dishman, A.F. / Tyler, R.C. / Fox, J.C. / Kleist, A.B. / Prehoda, K.E. / Babu, M.M. / Peterson, F.C. / Volkman, B.F.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jun 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 1.3Oct 30, 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: XCL1 ancestor


Theoretical massNumber of molelcules
Total (without water)7,4831
Polymers7,4831
Non-polymers00
Water00
1


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

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Components

#1: Protein XCL1 ancestor


Mass: 7483.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
141isotropic13D HNCO

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] Anc.0, 20 mM sodium phosphate, 0.02 % sodium azide, 95% H2O/5% D2O
Label: 15N/13C_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMAnc.0[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
0.02 %sodium azidenatural abundance1
Sample conditionsIonic strength: 29 mM / Label: Conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600.13 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 5
Details: Structure are based on a total of 1098 restraints, 1006 are NOE-derived distance contraints and 92 are dihedral angle restraints.
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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