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- PDB-2jq5: Solution structure of RPA3114, a SEC-C motif containing protein f... -

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Basic information

Entry
Database: PDB / ID: 2jq5
TitleSolution structure of RPA3114, a SEC-C motif containing protein from Rhodopseudomonas palustris; Northeast Structural Genomics Consortium target RpT5 / Ontario Center for Structural Proteomics target RP3097
ComponentsSEC-C motif
KeywordsSTRUCTURAL GENOMICS / Sec-c motif containing protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homologyYchJ, middle NTF2-like domain / SEC-C motif / SEC-C motif / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SEC-C motif
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / simulated annealing
AuthorsLemak, A. / Lukin, J. / Yee, A. / Gutmanas, A. / Karra, M. / Semesi, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution structure of a Se-C motif containing protein from Rhodopseudomonas palustris
Authors: Lemak, A. / Lukin, J. / Yee, A. / Gutmanas, A. / Karra, M. / Semesi, A. / Arrowsmith, C.H.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Database references
Revision 1.4Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 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: SEC-C motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7272
Polymers14,6611
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SEC-C motif


Mass: 14661.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA3114 / Plasmid: P11 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 de3 (gold magic) / References: UniProt: Q6N568
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCO
1513D H(CCO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1823D (H)CCH-TOCSY
1923D 1H-13C NOESY aliphatic
11023D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] RPA3114, 10 mM [U-99% 2H] TRIS, 10 mM [U-99% 2H] DTT, 300 mM sodium chloride, 0.1 % sodium azide, 1 mM benzamidine, 10 uM ZnS04, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-13C; U-15N] RPA3114, 10 mM [U-99% 2H] TRIS, 10 mM [U-99% 2H] DTT, 300 mM sodium chloride, 0.1 % sodium azide, 1 mM benzamidine, 10 uM ZnS04, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1[U-13C; U-15N]1
10 mMTRIS[U-99% 2H]1
10 mMDTT[U-99% 2H]1
300 mMsodium chloride1
0.1 %sodium azide1
1 mMbenzamidine1
10 uMZnS041
0.5 mMentity_1[U-13C; U-15N]2
10 mMTRIS[U-99% 2H]2
10 mMDTT[U-99% 2H]2
300 mMsodium chloride2
0.1 %sodium azide2
1 mMbenzamidine2
10 uMZnS042
Sample conditionsIonic strength: 300 mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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