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- PDB-2l3a: Solution NMR structure of homodimer protein SP_0782 (7-79) from S... -

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Basic information

Entry
Database: PDB / ID: 2l3a
TitleSolution NMR structure of homodimer protein SP_0782 (7-79) from Streptococcus pneumoniae Northeast Structural Genomics Consortium Target SpR104 .
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional Co-activator pc4; Chain A - #70 / PC4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein / PC4 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of hepothetical homodimer protein SP_0782 (7-79) from Streptococcus pneumoniae, Northeast Structural Genomics Consortium Target SpR104
Authors: Yang, Y. / Ramelot, T.A. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionSep 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 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 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,1862
Polymers19,1862
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)20 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 9592.798 Da / Num. of mol.: 2 / Fragment: sequence database residues 7-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_0782 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q97RM2, UniProt: A0A0H2UPA7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC CT
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HN(CO)CA
11013D HBHA(CO)NH
11113D H(CCO)NH
11213D C(CO)NH
11313D (H)CCH-TOCSY
11413D (H)CCH-COSY
11533D (H)CCH-TOCSY
11634D CC NOESY
11712D 1H-15N HSQC swN150ppm
11843D edited/filtered 13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] homodimer protein SP_0782 (7-79) from Streptococcus pneumoniae, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-5% 13C; U-100% 15N] homodimer protein SP_0782 (7-79) from Streptococcus pneumoniae, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM [U-100% 13C; U-100% 15N] homodimer protein SP_0782 (7-79) from Streptococcus pneumoniae, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
41.2 mM (1) [U-100% 13C; U-100% 15N]; (2) natural abundance homodimer protein SP_0782 (7-79) from Streptococcus pneumoniae, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMhomodimer protein SP_0782 (7-79) from Streptococcus pneumoniae-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
1.2 mMhomodimer protein SP_0782 (7-79) from Streptococcus pneumoniae-7[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
1.2 mMhomodimer protein SP_0782 (7-79) from Streptococcus pneumoniae-13[U-100% 13C; U-100% 15N]3
20 mMammonium acetate-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
10 mMDTT-173
0.02 %sodium azide-183
1.2 mMhomodimer protein SP_0782 (7-79) from Streptococcus pneumoniae-19(1) [U-100% 13C; U-100% 15N]; (2) natural abundance4
20 mMammonium acetate-204
100 mMsodium chloride-214
5 mMcalcium chloride-224
10 mMDTT-234
0.02 %sodium azide-244
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, A., Assadi, A., Markley, J. L. & Eghbalnia, H.autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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