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

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Basic information

Entry
Database: PDB / ID: 5kpe
TitleSolution NMR Structure of Denovo Beta Sheet Design Protein, Northeast Structural Genomics Consortium (NESG) Target OR664
ComponentsDe novo Beta Sheet Design Protein OR664
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsTang, Y. / Liu, G. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094597 United States
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 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references / Structure summary
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.6Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.7May 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 OR664


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
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 area7670 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 OR664


Mass: 13593.999 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
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D HN(COCA)CB
161isotropic13D SIMUTANEOUS 13C-AROMATIC,13C- ALIPHATIC,15N EDITED 1H-1H NOESY
171isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.27 mM [U-99% 13C; U-99% 15N] OR664, 90% H2O/10% D2O
Details: NC label samples, PBS (no DTT) - / Label: OR664.006 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.27 mM / Component: OR664 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: PBS buffer: 137 mM NaCl 2.7 mM KCl 10 mM Na2HPO4 1.8 mM KH2PO4 pH 7.4
Ionic strength: 140 mM / Ionic strength err: 1 / Label: conditions_1 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AutoStructureHuang, Tejero, Powers and Montelionestructure calculation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / 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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