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- PDB-2jqe: Soution Structure of Af54 M-domain -

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Basic information

Entry
Database: PDB / ID: 2jqe
TitleSoution Structure of Af54 M-domain
ComponentsSignal recognition 54 kDa protein
KeywordsSIGNALING PROTEIN / af54 / srp54 / solution
Function / homology
Function and homology information


signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding
Similarity search - Function
Signal recognition particle, SRP54 subunit, M-domain / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain ...Signal recognition particle, SRP54 subunit, M-domain / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / 434 Repressor (Amino-terminal Domain) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsIlangovan, U. / Hinck, A.P. / Zwieb, C.
CitationJournal: J.Biomol.Nmr / Year: 2008
Title: A. fulgidus SRP54 M-domain
Authors: Ilangovan, U. / Bhuiyan, S.H. / Hinck, C.S. / Hoyle, J.T. / Pakhomova, O.N. / Zwieb, C. / Hinck, A.P.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)13,7911
Polymers13,7911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Signal recognition 54 kDa protein / SRP54


Mass: 13790.513 Da / Num. of mol.: 1 / Fragment: SRP54 M-domain, residues 313-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: srp54 / Production host: Escherichia coli (E. coli) / References: UniProt: O29633

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNHA
1313D HNHB
1413D 1H-15N NOESY
1522D 1H-13C HSQC
1623D HN(CA)CB
1723D CBCA(CO)NH
1823D C(CO)NH
1923D (H)CCH-TOCSY
11023D 1H-13C NOESY
11123D HNCO
11223D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-95% 15N] af54, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-95% 13C; U-95% 15N] af54, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMaf54[U-95% 15N]1
0.5 mMaf54[U-95% 13C; U-95% 15N]2
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
NMRView5.0.4Johnson, One Moon Scientificdata analysis
NMRView5.0.4Johnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectral visualization
X-PLOR NIH2.9.6Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.9.6Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 724 / NOE intraresidue total count: 0 / NOE long range total count: 134 / NOE medium range total count: 284 / NOE sequential total count: 306
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 7.3 Å

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