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- PDB-2f40: Structure of a Novel Protein from Backbone-Centered NMR Data and ... -

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Basic information

Entry
Database: PDB / ID: 2f40
TitleStructure of a Novel Protein from Backbone-Centered NMR Data and NMR-Assisted Structure Prediction
Componentshypothetical protein PF1455
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure prediction / residual dipolar couplings / Pyrococcus furious / simulated annealing / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homologyUncharacterised protein PF11491 family, DUF3213 / Protein of unknown function DUF3213 / Protein of unknown function (DUF3213) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / : / DUF3213 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / RDC directed fragment assembly
AuthorsBansal, S. / Prestegard, J.H. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Proteins / Year: 2006
Title: Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction.
Authors: Mayer, K.L. / Qu, Y. / Bansal, S. / LeBlond, P.D. / Jenney, F.E. / Brereton, P.S. / Adams, M.W. / Xu, Y. / Prestegard, J.H.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PF1455


Theoretical massNumber of molelcules
Total (without water)11,2461
Polymers11,2461
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)10 / -
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein PF1455


Mass: 11245.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Plasmid: pRIL / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10, BL21(DE3) / References: GenBank: 18977827, UniProt: Q8U0X6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N IPAP HSQC
1213D 15N-separated NOESY
131HNCA-ECOSY
141HNCAHA
1513D TOCSY
26215N IPAP HSQC
272HNCA-ECOSY
38315N IPAP HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM PF1455 U-15N, 20mM Tris, 70mM NaCl, pH 7.0, 90% H20, 10% D2090% H20, 10% D20
21.14mM PF1455 U-15N/16%13C, 11mM Tris, 40mM NaCl, 10mg/ml Phage, Phage in 90% H2O, 10% D2OPhage in 90% H2O, 10% D2O
31.2mM PF1455 U-15N/16%13C, 20mM Tris, 70mM NaCl, 3% C12E5/hexanol, pH 7.0, C12E5 in 90% H2O, 10% D2OC12E5 in 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
170mM NaCl 7ambient 298 K
240mM NaCl 7ambient 298 K
370mM NaCl 7ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxdata analysis
XPLOR-NIH2.9.1refinement
REDCAT1Valafar, H. & Prestegard J.H.data analysis
RefinementMethod: RDC directed fragment assembly / Software ordinal: 1
Details: limited amounts of structural data are used to improve an initial homology search and the data are subsequently used to produce a structure by data-constrained refinement of an identified structural template
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers submitted total number: 10

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