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- PDB-2mtl: Solution NMR Structure of De novo designed FR55, Northeast Struct... -

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Basic information

Entry
Database: PDB / ID: 2mtl
TitleSolution NMR Structure of De novo designed FR55, Northeast Structural Genomics Consortium (NESG) Target OR109
ComponentsDe novo designed protein FR55 OR109
KeywordsDE NOVO PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homologyRibosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesArtificial gene (others)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsLiu, G. / Koga, N. / Koga, R. / Xiao, R. / Hamilton, K. / Ciccosanti, C. / Sahdev, S. / Kohan, E. / Acton, T.B. / Kornhaber, G. ...Liu, G. / Koga, N. / Koga, R. / Xiao, R. / Hamilton, K. / Ciccosanti, C. / Sahdev, S. / Kohan, E. / Acton, T.B. / Kornhaber, G. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of De novo designed FR55, Northeast Structural Genomics Consortium (NESG) Target OR109
Authors: Liu, G. / Koga, N. / Koga, R. / Xiao, R. / Hamilton, K. / Ciccosanti, C. / Sahdev, S. / Kohan, E. / Acton, T.B. / Kornhaber, G. / Everett, J.K. / Baker, D. / Montelione, G.T.
History
DepositionAug 19, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 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
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed protein FR55 OR109


Theoretical massNumber of molelcules
Total (without water)10,2341
Polymers10,2341
Non-polymers00
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein De novo designed protein FR55 OR109


Mass: 10233.644 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
1813D CCH-TOCSY
1912D 1H-13C HSQC aliphatic
11012D 1H-15N HSQC

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Sample preparation

DetailsContents: 1.01 mM OR109.009, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 308 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 Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
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
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TopSpinBruker Biospincollection
VnmrJVariancollection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
REDCATValafar, Prestegardgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: distance geometry, simulated annealing, 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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