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- PDB-1kvv: Solution Structure Of Protein SRP19 Of The Archaeoglobus fulgidus... -

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Basic information

Entry
Database: PDB / ID: 1kvv
TitleSolution Structure Of Protein SRP19 Of The Archaeoglobus fulgidus Signal Recognition Particle, Minimized Average Structure
ComponentsSRP19
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle / 7S RNA binding
Similarity search - Function
Signal recognition particle, SRP19 subunit, archaeal-type / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / Distance geometry, simulated annealing protocol
Model type detailsminimized average
AuthorsPakhomova, O.N. / Deep, S. / Huang, Q. / Zwieb, C. / Hinck, A.P.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Solution structure of protein SRP19 of Archaeoglobus fulgidus signal recognition particle.
Authors: Pakhomova, O.N. / Deep, S. / Huang, Q. / Zwieb, C. / Hinck, A.P.
History
DepositionJan 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SRP19


Theoretical massNumber of molelcules
Total (without water)12,4071
Polymers12,4071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein SRP19 / SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN


Mass: 12406.707 Da / Num. of mol.: 1 / Mutation: C4S/C41S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1258 / Plasmid: pET-23c(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29010

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1324D 13C-separated NOESY
1413D 15N-separated NOESY with 13C chemical shift evolution in F2 dimension
251IPAP-HSQC
NMR detailsText: IPAP-HSQC experiment was performed in a sample of the protein in either an unstressed or mechanically stressed 8% polyacrylamide gel.

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Sample preparation

Details
Solution-IDContentsSolvent system
125mM KH2PO4, 50mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
225mM KH2PO4, 50mM NaCl, 99.99% D2O99.99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
175 mM 6ambient 300 K
275 mM 6ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX2 / Manufacturer: Bruker / Model: AMX2 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Bruker analytic GmbHcollection
NMRPipe1.8Delaglio,F., Grzesiek, S., Vuister, G., Zhu, W., Pfeifer, J., Bax, A.processing
PIPP4.3.1Garrett, D. C., Powers, R., Gronenborn, A.M., Clore, G. M.data analysis
X-PLOR3.851Brunger, A. T.; Clore, G.M., Gronenborn, A.M., Tjundra, N.structure solution
TALOS98.040.28.02Cornilescu, G., Delaglio, F., Bax, A.data analysis
PALES2.1Zweckstetter, M., Bax, A.data analysis
X-PLOR3.851Brunger, A.T.; Clore, G.M., Gronenborn, A.M., Tjundra, N.refinement
RefinementMethod: Distance geometry, simulated annealing protocol / Software ordinal: 1
Details: The structures are based on a total of 886 restraints, 690 are NOE-derived distance constraints, 130 dihegral angle restraints, 66 1H-15N residual dipolar coupling restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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