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- PDB-2n2u: Solution NMR Structure of DE NOVO DESIGNED Ferredoxin Fold PROTEI... -

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Basic information

Entry
Database: PDB / ID: 2n2u
TitleSolution NMR Structure of DE NOVO DESIGNED Ferredoxin Fold PROTEIN sfr3, Northeast Structural Genomics Consortium (NESG) Target OR358
ComponentsOR358
KeywordsUnknown Function / Structural Genomics / Protein NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Target OR358 / PSI-Biology / Protein Structure Initiative
Biological speciesSynthetic construct (others)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, null
Model detailslowest energy, model1
AuthorsLiu, G. / Lin, Y. / Koga, N. / Koga, R. / Xiao, R. / Janjua, H. / Hamilton, K. / Pederson, K. / Acton, T.B. / Kornhaber, G. ...Liu, G. / Lin, Y. / Koga, N. / Koga, R. / Xiao, R. / Janjua, H. / Hamilton, K. / Pederson, K. / 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 Ferredoxin Fold PROTEIN sfr3, Northeast Structural Genomics Consortium (NESG) Target OR358
Authors: Liu, G. / Lin, Y. / Koga, N. / Koga, R. / Xiao, R. / Janjua, H. / Hamilton, K. / Pederson, K. / Acton, T.B. / Kornhaber, G. / Everett, J.K. / Baker, D. / Montelione, G.T.
History
DepositionMay 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: 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: OR358


Theoretical massNumber of molelcules
Total (without water)8,8981
Polymers8,8981
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 OR358


Mass: 8898.082 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) / 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
1132D 1H-15N HSQC
1212D 1H-13C HSQC
1333D HNCO
1433D CBCA(CO)NH
1533D HN(CA)CB
1633D 1H-13C arom NOESY
1733D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1833D CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.787 mM OR358.006, 90% H2O/10% D2O90% H2O/10% D2O
20.787 mM OR358.006, 90% H2O/10% D2O90% H2O/10% D2O
30.787 mM OR358.006, 90% H2O/10% D2O90% H2O/10% D2O
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 Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis,peak picking,chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
REDCATValafar, Prestegardgeometry optimization
PSVSBhattacharya, Montelionestructure validation
CYANAHuang, Tejero, Powers and Montelionerefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, null
Software ordinal: 1 / Details: null, null
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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