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- PDB-5kph: Solution NMR Structure of Denovo Beta Sheet Design Protein, North... -

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Basic information

Entry
Database: PDB / ID: 5kph
TitleSolution NMR Structure of Denovo Beta Sheet Design Protein, Northeast Structural Genomics Consortium (NESG) Target OR485
ComponentsDe novo Beta Sheet Design Protein OR485
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing, distance geometry, molecular dynamics
AuthorsTang, Y. / Liu, G. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Science / Year: 2017
Title: Principles for designing proteins with cavities formed by curved beta sheets.
Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / ...Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / Montelione, G.T. / Baker, D.
History
DepositionJul 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_struct_assembly_auth_evidence / Item: _entity.pdbx_number_of_molecules
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo Beta Sheet Design Protein OR485


Theoretical massNumber of molelcules
Total (without water)10,0971
Polymers10,0971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6540 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy
DetailsMonomer as determined by light scattering.

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Components

#1: Protein De novo Beta Sheet Design Protein OR485


Mass: 10097.393 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
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D HN(COCA)CB
161isotropic13D SIMUTANEOUS 13C-AROMATIC, 13-CALIPHATIC,15N EDITED 1H-1H NOESY
171isotropic13D 13C-AROMATIC NOESY

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Sample preparation

DetailsType: solution
Contents: 0.80 mM [U-99% 13C; U-99% 15N] OR485, 90% H2O/10% D2O
Details: Low Salt, 5 mM DTT 100 mM NaCl 10 mM Tris-HCl pH 7.5 0.02 % NaN3, volume:0.3 mL; protein concentration:0.80 mM
Label: OR485.004 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.80 mM / Component: OR485 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: Low Salt, 5 mM DTT 100 mM NaCl 10 mM Tris-HCl pH 7.5 0.02 % NaN3, volume:0.3 mL; protein concentration:0.80 mM
Ionic strength: 100 mM / Ionic strength err: 1 / Label: conditions_1 / pH: 7.5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.peak picking
AutoStructureHuang, Tejero, Powers and Montelionerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, distance geometry, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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