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- PDB-1rws: Backbone Solution Structure of mixed alpha/beta protein PF1061 -

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Basic information

Entry
Database: PDB / ID: 1rws
TitleBackbone Solution Structure of mixed alpha/beta protein PF1061
Componentshypothetical protein PF1061Hypothesis
KeywordsUNKNOWN FUNCTION / residual dipolar couplings / structural genomics
Function / homology
Function and homology information


Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Small archaeal modifier protein 2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / RDC directed fragment assembly
AuthorsPrestegard, J.H. / Mayer, K.L. / Valafar, H.
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2004
Title: Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target.
Authors: Valafar, H. / Mayer, K.L. / Bougault, C.M. / LeBlond, P.D. / Jenney, F.E. / Brereton, P.S. / Adams, M.W. / Prestegard, J.H.
History
DepositionDec 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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 PF1061


Theoretical massNumber of molelcules
Total (without water)8,6111
Polymers8,6111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1fewest violations

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Components

#1: Protein hypothetical protein PF1061 / Hypothesis


Mass: 8610.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1061 / Plasmid: pET24d Bam / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3Star pRIL / References: UniProt: Q8U1Z3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111soft HNCA-E.COSY
121modified HNCO
13115N coupled HSQC
1413D 15N-separated NOESY
1513D 15N-separated TOCSY
262soft HNCA-E.COSY
272modified HNCO
28215N coupled HSQC
393soft HNCA-E.COSY
310315N coupled HSQC
NMR detailsText: This structure was determined using predominantly residual dipolar couplings from backbone atom pairs. It is a backbone structure modeled as an Ala-Gly-Pro polypeptide.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 1016054 U-15N, 16% 13C; 50 mM phosphate buffer; 200 mM KCl; 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM 1016054 U-15N, 16% 13C; 50 mM phosphate buffer; 100 mM KCl; PEG bicelles (C12E5-hexanol in 0.98 ratio); 90% H2O, 10% D2OPEG bicelles (C12E5-hexanol in 0.98 ratio); 90% H2O, 10% D2O
30.5 mM 1016054 U-15N, 16% 13C; 50 mM phosphate buffer; 100 mM KCl; PEG-CTAB (27:1)bicelles (C12E5-hexanol in 0.87 ratio); 90% H2O, 10% D2OPEG-CTAB (27:1)bicelles (C12E5-hexanol in 0.87 ratio); 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200 mM KCl 5.5 ambient 298 K
2100 mM KCl 6 ambient 300 K
3100 mM KCl 6 ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe5.0.4F. DeLaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer and A. Baxdata analysis
REDcRAFT1H. Valafar, J. Prestegardstructure solution
XPLOR-NIH2.9.1Schwieters, Kuszewski, Tjandra, Clorerefinement
REDCAT1H. Valafar, J. Prestegarddata analysis
RefinementMethod: RDC directed fragment assembly / Software ordinal: 1
Details: RDCs were used in the initial assembly of four fragments. RDCs from two media were used to set relative orientations of the fragments. Translational relationships of fragments were dictated ...Details: RDCs were used in the initial assembly of four fragments. RDCs from two media were used to set relative orientations of the fragments. Translational relationships of fragments were dictated by sequence connectivities and long-range NOEs. The assembled structure was minimized using a molecular force field and RDC error function. A total of 486 restraints were used: 380 residual dipolar coupling restraints, 85 NOE restraints (of which 64 were sequential, 11 short-range and 10 long-range), and 21 dihedral restraints. All sidechain atoms beyond CB are missing.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformers submitted total number: 1

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