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- PDB-6y07: Designing a Granulopoietic Protein by Topological Rescaffolding 1... -

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Basic information

Entry
Database: PDB / ID: 6y07
TitleDesigning a Granulopoietic Protein by Topological Rescaffolding 1: Sohair
Componentssohair
KeywordsDE NOVO PROTEIN / protein design / receptor modulator / GCSF analog
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / NOESY back-calculation
AuthorsElGamacy, M. / Coles, M.
Citation
Journal: Plos Biol. / Year: 2020
Title: Design of novel granulopoietic proteins by topological rescaffolding.
Authors: Hernandez Alvarez, B. / Skokowa, J. / Coles, M. / Mir, P. / Nasri, M. / Maksymenko, K. / Weidmann, L. / Rogers, K.W. / Welte, K. / Lupas, A.N. / Muller, P. / ElGamacy, M.
#1: Journal: Structure / Year: 2019
Title: Mapping Local Conformational Landscapes of Proteins in Solution.
Authors: ElGamacy, M. / Riss, M. / Zhu, H. / Truffault, V. / Coles, M.
History
DepositionFeb 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sohair


Theoretical massNumber of molelcules
Total (without water)20,2971
Polymers20,2971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 20000back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1medoid

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Components

#1: Protein sohair


Mass: 20297.090 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
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D (H)CC(CO)NH
141isotropic13D H(CCO)NH
151isotropic13D CCH-TOCSY
161isotropic22D NOESY
171isotropic23D CNH-NOESY
181isotropic23D 1H-15N NOESY
191isotropic23D NNH-NOESY

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Sample preparation

DetailsType: solution
Contents: 650 uM [U-99% 13C; U-99% 15N] sohair, 50 mM PBS, 90% H2O/10% D2O
Label: double labelled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
650 uMsohair[U-99% 13C; U-99% 15N]1
50 mMPBSnatural abundance1
Sample conditionsIonic strength: 125 mM / Label: conditions_1 / pH: 5.2 / Pressure: 1 atm / Temperature: 315 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospindata analysis
SparkyGoddardchemical shift assignment
RosettaBakerstructure calculation
CoMANDin houserefinement
RefinementMethod: NOESY back-calculation / Software ordinal: 4
Details: see (2019) ElGamacy et al., Structure 27: 853-865.e5
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 20000 / Conformers submitted total number: 19

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