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- PDB-2kjp: Solution structure of protein YlbL (BSU15050) from Bacillus subti... -

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Basic information

Entry
Database: PDB / ID: 2kjp
TitleSolution structure of protein YlbL (BSU15050) from Bacillus subtilis, Northeast Structural Genomics Consortium target sr713a
ComponentsUncharacterized protein ylbL
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / mixed alpha-beta protein / Cell membrane / Hydrolase / Membrane / Protease / Serine protease / Transmembrane / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


ATP-dependent peptidase activity / protein catabolic process / membrane => GO:0016020 / serine-type endopeptidase activity / ATP binding / plasma membrane
Similarity search - Function
Endopeptidase La, PDZ domain / PDZ domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Endopeptidase La, PDZ domain / PDZ domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Roll / Ribosomal protein S5 domain 2-type fold / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein YlbL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 10
AuthorsLiu, Y. / Belote, R. / Ciccosanti, C. / Hamilton, K. / Nair, R. / Rost, B. / Acton, T. / Xiao, R. / Swapna, G. / Everett, J. ...Liu, Y. / Belote, R. / Ciccosanti, C. / Hamilton, K. / Nair, R. / Rost, B. / Acton, T. / Xiao, R. / Swapna, G. / Everett, J. / Montelione, G.T. / Prestegard, J. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of protein YlbL (BSU15050) from Bacillus subtilis, Northeast Structural Genomics Consortium target sr713a
Authors: Liu, Y. / Belote, R. / Ciccosanti, C. / Hamilton, K. / Nair, R. / Rost, B. / Acton, T. / Xiao, R. / Swapna, G. / Everett, J. / Montelione, G.T. / Prestegard, J.
History
DepositionJun 5, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein ylbL


Theoretical massNumber of molelcules
Total (without water)10,1841
Polymers10,1841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 90structures with the lowest energy
RepresentativeModel #10lowest energy

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Components

#1: Protein Uncharacterized protein ylbL


Mass: 10183.506 Da / Num. of mol.: 1 / Fragment: sequence database residues 128-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ylbL, BSU15050 / Production host: Escherichia coli (E. coli) / References: UniProt: O34470

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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 CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D H(CCO)NH
1613D C(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11023D 1H-13C NOESY
1113TROSY-HSQC
1123TROSY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 100 mM DTT, 3 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 5 mM DTT, 3 mM sodium azide, 100% D2O100% D2O
30.5 mM [U-99% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 100 mM DTT, 3 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-99% 13C; U-99% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
100 mMDTT-51
3 mMsodium azide-61
0.5 mMprotein-7[U-99% 13C; U-99% 15N]2
20 mMMES-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
5 mMDTT-112
3 mMsodium azide-122
0.5 mMprotein-13[U-99% 15N]3
20 mMMES-143
200 mMsodium chloride-153
5 mMcalcium chloride-163
100 mMDTT-173
3 mMsodium azide-183
Sample conditionsIonic strength: 0.3 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The pseudo atoms labeled ANI are included in the constraint file. These define an alignment frame used in the structural interpretation of RDC data.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 90 / Conformers submitted total number: 21

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