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- PDB-5gaj: Solution NMR structure of De novo designed PLOOP2X3_50 fold prote... -

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Basic information

Entry
Database: PDB / ID: 5gaj
TitleSolution NMR structure of De novo designed PLOOP2X3_50 fold protein, Northeast Structural Genomics Consortium (NESG) target OR258
ComponentsDE NOVO DESIGNED PROTEIN OR258
KeywordsDE NOVO PROTEIN / Northeast Structural Genomics Consortium / NESG / PSI-Biology
Function / homologyRossmann fold - #11230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsLiu, G. / Castelllanos, J. / Koga, R. / Koga, N. / Xiao, R. / Pederson, K. / Janjua, H. / Kohan, E. / Acton, T.B. / Kornhaber, G. ...Liu, G. / Castelllanos, J. / Koga, R. / Koga, N. / Xiao, R. / Pederson, K. / Janjua, H. / Kohan, E. / Acton, T.B. / Kornhaber, G. / Everett, J. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To Be Published
Title: Solution NMR structure De novo designed PLOOP2X3_50 fold protein, Northeast Structural Genomics Consortium (NESG) target OR258
Authors: Liu, G. / Montelione, G.T.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_prerelease_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 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:
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Assembly

Deposited unit
A: DE NOVO DESIGNED PROTEIN OR258


Theoretical massNumber of molelcules
Total (without water)15,7691
Polymers15,7691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein DE NOVO DESIGNED PROTEIN OR258


Mass: 15769.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D simutalneous 13C-aromatic, 13C-aliphatic, 15N edited 1H-1H NOESY
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D HN(CA)CB
141isotropic13D CCH-TOCSY
151isotropic12D 1H-15N HSQC
161isotropic12D 1H-13C HSQC aliphatic
172isotropic12D 1H-13C HSQC methyl

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.89 mM [U-13C; U-15N] OR258, 5 mM DTT, 100 mM sodium chloride, 10 mM TRIS-HCl, 0.02 % sodium azide, 90% H2O/10% D2OLow Salt - 5 mM DTT 100 mM NaCl 10 mM Tris-HCl pH 7.5 0.02 % NaN3NC_sample90% H2O/10% D2O
solution20.89 mM [5%-13C; U-15N] OR258, 5 mM DTT, 100 mM sodium chloride, 10 mM TRIS-HCl, 0.02 % sodium azide, 90% H2O/10% D2OLow Salt - 5 mM DTT 100 mM NaCl 10 mM Tris-HCl pH 7.5 0.02 % NaN3NC5_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.89 mMOR258[U-13C; U-15N]1
5 mMDTTnatural abundance1
100 mMsodium chloridenatural abundance1
10 mMTRIS-HClnatural abundance1
0.02 %sodium azidenatural abundance1
0.89 mMOR258[5%-13C; U-15N]2
5 mMDTTnatural abundance2
100 mMsodium chloridenatural abundance2
10 mMTRIS-HClnatural abundance2
0.02 %sodium azidenatural abundance2
Sample conditionsIonic strength: 115 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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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
RefinementMethod: 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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