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- PDB-1lq7: De Novo Designed Protein Model of Radical Enzymes -

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Basic information

Entry
Database: PDB / ID: 1lq7
TitleDe Novo Designed Protein Model of Radical Enzymes
ComponentsAlpha3W
KeywordsDE NOVO PROTEIN / three helix bundle
Function / homologyDesigned single chain three-helix bundle / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDai, Q.-H. / Tommos, C. / Fuentes, E.J. / Blomberg, M. / Dutton, P.L. / Wand, A.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2002
Title: Structure of a De Novo Designed Protein Model of Radical Enzymes
Authors: Dai, Q.-H. / Tommos, C. / Fuentes, E.J. / Blomberg, M. / Dutton, P.L. / Wand, A.J.
#1: Journal: Biochemistry / Year: 1999
Title: De novo proteins as models of radical enzymes
Authors: Tommos, C. / Skalicky, J.J. / Pilloud, D.L. / Wand, A.J. / Dutton, P.L.
History
DepositionMay 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999sequence an appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha3W


Theoretical massNumber of molelcules
Total (without water)7,5631
Polymers7,5631
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)16 / 30lowest refinement function penalty, best chemical shift agreement
RepresentativeModel #16chemical shift

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Components

#1: Protein Alpha3W


Mass: 7562.899 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein model for tryptophanyl radical
Description: de novo design/synthetic gene: gene generated using overlapping PCR method from synthetic oligos
Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 13C-separated NOESY
1324D 13C-separated NOESY
141HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.85 mM U-15N,13C-a3w, 20 mM acetate, 50 mM KCl92% H2O/8% D2O
20.85 mM U-15N,13C-a3w, 20 mM acetate, 50 mM KCl2% H2O/98% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
170 mM 5.5ambient 301 K
270 mM 5.5ambient 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR softwareName: DYANA / Version: 1.5 / Developer: Gntert, C. Mumenthaler, K. Wuthrich / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: 1130 NOEs, 43 phi restraints
NMR representativeSelection criteria: chemical shift
NMR ensembleConformer selection criteria: lowest refinement function penalty, best chemical shift agreement
Conformers calculated total number: 30 / Conformers submitted total number: 16

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