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- PDB-6ns8: RDC-refined SOLUTION NMR STRUCTURE OF PROTEIN PF2048.1 -

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Basic information

Entry
Database: PDB / ID: 6ns8
TitleRDC-refined SOLUTION NMR STRUCTURE OF PROTEIN PF2048.1
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsDaigham, N.S. / Liu, G. / Swapna, G.V.T. / Cole, C. / Valafar, H. / Montelione, G.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: REDCRAFT: A Computational Platform Using Residual Dipolar Coupling NMR Data for Determining Structures of Perdeuterated Proteins Without NOEs
Authors: Daigham, N.S. / Liu, G. / Swapna, G.V.T. / Cole, C. / Valafar, H. / Montelione, G.T.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Experimental preparation / Structure summary
Category: citation / pdbx_nmr_details / struct / Item: _citation.title / _struct.title
Revision 1.2May 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)9,3531
Polymers9,3531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein Uncharacterized protein


Mass: 9352.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_08315 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I6V394

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic
Type: 3D SIMULTANEOUS 13C-AROMATIC,13C-ALIPHATIC,15N EDITED 1H-1H NOESY
NMR detailsText: The authors state that the medoid structure is conformer model 13

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] PF2048.1, 90% H2O/10% D2O
Details: 0.8 MM [U-100% 13C; U-100% 15N] PF2048.1, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 NA CALCIUM CHLORIDE, 0.02 % SODIUM AZIDE, 10 % DSS, 90% H2O/10% D2O
Label: NC / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: PF2048.1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: NC / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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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
SparkyGoddardpeak picking
AutoStructureHuang, Tejero, Powers and Montelionerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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