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- PDB-2p0x: solution structure of a non-biological ATP-binding protein -

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Basic information

Entry
Database: PDB / ID: 2p0x
Titlesolution structure of a non-biological ATP-binding protein
Componentsabiotic ATP-binding, folding optimized protein
KeywordsDE NOVO PROTEIN / alpha/beta fold / treble clef zinc binding motif
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciessynthetic gene (others)
MethodSOLUTION NMR / hybrid distance geometry - simulated annealing
AuthorsMansy, S.S. / Szostak, J.W. / Chaput, J.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Evolutionary Analysis of a Non-biological ATP-binding Protein
Authors: Mansy, S.S. / Zhang, J. / Kummerle, R. / Nilsson, M. / Chou, J.J. / Szostak, J.W. / Chaput, J.C.
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: abiotic ATP-binding, folding optimized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1003
Polymers7,5281
Non-polymers5732
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein abiotic ATP-binding, folding optimized protein


Mass: 7527.653 Da / Num. of mol.: 1 / Mutation: C58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic gene (others)
Description: synthetic gene, abiotic protein selected by mRNA-display
Plasmid: pIADL14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA-J
1213D 15N-separated NOESY
131HNHA
141TROSY-HNCO
151(H)CCH-TOCSY
161HN(CA)CB

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Sample preparation

DetailsContents: 0.3 mM folding optimized protein U-15N,13C; 10 mM sodium phosphate, 50 mM KCl, 0.5 mM ATP, pH 6.5; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.064 M / pH: 6.5 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH 2.13Brunger A. T. et alstructure solution
NMRPipe2006Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J. & Bax, A.processing
Bruker TopSpin1.3Bruker BioSpinprocessing
X-PLORNIH 2.13Brunger A. T. et alrefinement
RefinementMethod: hybrid distance geometry - simulated annealing / Software ordinal: 1
Details: 673 distance restraints, 60 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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