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- PDB-2kjk: Solution structure of the second domain of the listeria protein L... -

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Basic information

Entry
Database: PDB / ID: 2kjk
TitleSolution structure of the second domain of the listeria protein Lin2157, Northeast Structural Genomics Consortium target Lkr136b
ComponentsLin2157 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ domain / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding / membrane
Similarity search - Function
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 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 / Ribosomal protein S5 domain 2-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsWang, X. / Hamilton, K. / Xiao, R.H. / Lee, D. / Ciccosanti, C.H. / Nair, R. / Rost, B. / Acton, T.B. / Swapna, G. / Everett, J.K. ...Wang, X. / Hamilton, K. / Xiao, R.H. / Lee, D. / Ciccosanti, C.H. / Nair, R. / Rost, B. / Acton, T.B. / Swapna, G. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of Lkr136b
Authors: Wang, X. / Montelione, G.T. / Prestegard, J.
History
DepositionMay 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 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 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin2157 protein


Theoretical massNumber of molelcules
Total (without water)11,0801
Polymers11,0801
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 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Lin2157 protein


Mass: 11079.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2157 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q929W6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D C(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1812D HSQC/TROSY
1922D HSQC/TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.18 mM [U-100% 13C; U-100% 15N] lkr136b, 10 mM DTT, 0.02 % sodium azide, 200 mM sodium chloride, 20 mM sodium acetate, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.18 mM [U-100% 13C; U-100% 15N] lkr136b, 4 % pentaethylene glycol monododecyl ether, 200 mM sodium chloride, 0.02 % sodium azide, 10 mM DTT, 20 mM sodium acetate, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.18 mMlkr136b-1[U-100% 13C; U-100% 15N]1
10 mMDTT-21
0.02 %sodium azide-31
200 mMsodium chloride-41
20 mMsodium acetate-51
5 mMcalcium chloride-61
1.18 mMlkr136b-7[U-100% 13C; U-100% 15N]2
4 %pentaethylene glycol monododecyl ether-82
200 mMsodium chloride-92
0.02 %sodium azide-102
10 mMDTT-112
20 mMsodium acetate-122
5 mMcalcium chloride-132
Sample conditionsIonic strength: 0.2 / pH: 4.5 / 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: structures were first calculated using CYANA's automatic NOE assignment module, which is simulated annealing based. They were then refined in XPLOR-NIH using simulated annealing refinement protocol
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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