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- PDB-2ln3: Solution NMR Structure of DE NOVO DESIGNED PROTEIN, IF3-like fold... -

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Basic information

Entry
Database: PDB / ID: 2ln3
TitleSolution NMR Structure of DE NOVO DESIGNED PROTEIN, IF3-like fold, Northeast Structural Genomics Consortium Target OR135 (CASD target)
ComponentsDE NOVO DESIGNED PROTEIN OR135
KeywordsDE NOVO PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologyTranslation Initiation Factor IF3 - #140 / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Koga, R. / Koga, N. / Xiao, R. / Lee, H. / Janjua, H. / Kohan, E. / Acton, T.B. / Everett, J.K. / Baker, D. ...Liu, G. / Koga, R. / Koga, N. / Xiao, R. / Lee, H. / Janjua, H. / Kohan, E. / Acton, T.B. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nature / Year: 2012
Title: Principles for designing ideal protein structures.
Authors: Koga, N. / Tatsumi-Koga, R. / Liu, G. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionDec 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references / Structure summary
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 7, 2012Group: Database references
Revision 1.4Jan 23, 2013Group: Database references
Revision 1.5Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DE NOVO DESIGNED PROTEIN OR135


Theoretical massNumber of molelcules
Total (without water)9,7971
Polymers9,7971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 OR135


Mass: 9797.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1822D 1H-13C HSQC aliphatic
1922D 1H-15N HSQC
11023D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.04 mM [U-100% 13C; U-100% 15N] OR135, 95% H2O/5% D2O95% H2O/5% D2O
21.14 mM [U-5% 13C; U-100% 15N] OR135, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.04 mMOR135-1[U-100% 13C; U-100% 15N]1
1.14 mMOR135-2[U-5% 13C; U-100% 15N]2
1.14 mMOR135-3[U-5% 13C; U-100% 15N]3
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
TopSpinBruker Biospincollection
VnmrJVariancollection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
REDCATValafar, Prestegardgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionerefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
RefinementMethod: simulated annealing, molecular dynamics, distance geometry, torsion angle 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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