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- PDB-2jua: Assignment, structure, and dynamics of de novo designed protein S836 -

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Basic information

Entry
Database: PDB / ID: 2jua
TitleAssignment, structure, and dynamics of de novo designed protein S836
Componentsde novo protein S836
KeywordsDE NOVO PROTEIN
Function / homologyDesigned four-helix bundle protein / hypothetical protein mp506/mpn330, domain 1 / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesunidentified (others)
MethodSOLUTION NMR / simulated annealing
AuthorsGo, A. / Kim, S. / Baum, J.S. / Hecht, M.H.
Citation
Journal: Protein Sci. / Year: 2008
Title: Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles.
Authors: Go, A. / Kim, S. / Baum, J. / Hecht, M.H.
#1: Journal: To be Published
Title: NMR assignment of S836: a de novo Protein from a Designed Protein Superfamily
Authors: Go, A. / Kim, S. / Hecht, M.H. / Baum, J.S.
History
DepositionAug 16, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999Sequence This is a de novo Protein design sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo protein S836


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
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 de novo protein S836


Mass: 11946.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ambiguous conformational states: Y2, Q24, and N84 register possible alternate alpha carbon chemical shifts
Source: (gene. exp.) unidentified (others) / Plasmid: pet3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D C(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D H(CCO)NH
1923D (H)CCH-TOCSY
11013D HNHA
11113D 1H-15N NOESY
11213D 1H-15N TOCSY
11323D 1H-13C NOESY
11423D (HCA)CO(CA)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-15N] S836, 10 % [U-2H] D2O, 50 mM acetic acid - sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-13C; U-15N] S836, 10 % [U-2H] D2O, 50 mM [U-13C] acetic acid - sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMS836[U-15N]1
10 %D2O[U-2H]1
50 mMacetic acid - sodium acetate1
2 mMS836[U-13C; U-15N]2
10 %D2O[U-2H]2
50 mMacetic acid - sodium acetate[U-13C]2
Sample conditionspH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.processing
SparkyGoddard, T.D. et al.data analysis
NMRDrawDelaglio, F. et al.data analysis
X-PLOR NIHSchwieters, C.D. et al.structure solution
X-PLOR NIHSchwieters, C.D. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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