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- PDB-2kl8: Solution NMR Structure of de novo designed ferredoxin-like fold p... -

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Basic information

Entry
Database: PDB / ID: 2kl8
TitleSolution NMR Structure of de novo designed ferredoxin-like fold protein, Northeast Structural Genomics Consortium Target OR15
ComponentsOR15
KeywordsDE NOVO PROTEIN / Structural Genomics / Protein NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Target OR15 / PSI-2 / Protein Structure Initiative / FERRODOXIN FOLD
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 detailsfewest violations, model 1
AuthorsLiu, G. / Koga, N. / Jiang, M. / Koga, R. / Xiao, R. / Ciccosanti, C. / 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
DepositionJun 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 7, 2012Group: Database references
Revision 1.4Jan 23, 2013Group: Database references
Revision 1.5Feb 26, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OR15


Theoretical massNumber of molelcules
Total (without water)10,0661
Polymers10,0661
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 #1fewest violations

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Components

#1: Protein OR15


Mass: 10066.479 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)+ Magic

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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 CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D H(CCO)NH
1813D HN(CO)CA
1913D simutaneous 1H, 15N, 13C NOESY

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Sample preparation

DetailsContents: 0.47 mM [U-100% 13C; U-100% 15N] OR15, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 0.47 mM / Component: OR15-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
AutoStructureHuang, Tejero, Powers and Montelionerefinement
AutoStructureHuang, Tejero, Powers and Montelionedata analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionedata analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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