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- PDB-2kl1: Solution structure of GtR34C from Geobacillus thermodenitrificans... -

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Basic information

Entry
Database: PDB / ID: 2kl1
TitleSolution structure of GtR34C from Geobacillus thermodenitrificans. Northeast Structural Genomics Consortium Target GtR34C
ComponentsYlbL protein
KeywordsPROTEIN BINDING / Structure Genomics / Structural Genomics / 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 / membrane => GO:0016020 / serine-type endopeptidase activity / ATP binding
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 speciesGeobacillus thermodenitrificans (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsLee, H. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G. / Evertt, J.K. ...Lee, H. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G. / Evertt, J.K. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of GtR34C
Authors: Lee, H. / Montelione, G.T. / Prestegard, J.H.
History
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / 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: YlbL protein


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 YlbL protein


Mass: 10581.041 Da / Num. of mol.: 1 / Fragment: sequence database residues 125-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Strain: NG80-2 / Gene: ylbL, GTNG_0967 / Production host: Geobacillus thermodenitrificans (bacteria) / References: UniProt: A4ILZ1

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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 C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D 1H-13C NOESY
11322D 15N HSQCTROSY
11432D 15N HSQCTROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.14 mM [U-100% 13C; U-100% 15N] GtR34C, 2 % sodium azide, 10 mM DTT, 5 mM CaCl, 200 mM sodium chloride, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
21.14 mM [U-100% 13C; U-100% 15N] GtR34C, 2 % sodium azide, 10 mM DTT, 5 mM CaCl, 200 mM sodium chloride, 20 mM MES, 4.2 % C12E5 PEG/Hexanol, 95% H2O/5% D2O95% H2O/5% D2O
31.14 mM [U-100% 13C; U-100% 15N] GtR34C, 2 % sodium azide, 10 mM DTT, 5 mM CaCl, 200 mM sodium chloride, 20 mM MES, 7 % Negatively Charged Compressed Polyacrylamide Gel-20, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.14 mMGtR34C-1[U-100% 13C; U-100% 15N]1
2 %sodium azide-21
10 mMDTT-31
5 mMCaCl-41
200 mMsodium chloride-51
20 mMMES-61
1.14 mMGtR34C-7[U-100% 13C; U-100% 15N]2
2 %sodium azide-82
10 mMDTT-92
5 mMCaCl-102
200 mMsodium chloride-112
20 mMMES-122
4.2 %C12E5 PEG/Hexanol-132
1.14 mMGtR34C-14[U-100% 13C; U-100% 15N]3
2 %sodium azide-153
10 mMDTT-163
5 mMCaCl-173
200 mMsodium chloride-183
20 mMMES-193
7 %Negatively Charged Compressed Polyacrylamide Gel-203
Sample conditionsIonic strength: 200 / 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
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionedata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
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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