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- PDB-2krs: Solution NMR structure of SH3 domain from CPF_0587 (fragment 415-... -

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Basic information

Entry
Database: PDB / ID: 2krs
TitleSolution NMR structure of SH3 domain from CPF_0587 (fragment 415-479) from Clostridium perfringens. Northeast Structural Genomics Consortium (NESG) Target CpR74A.
ComponentsProbable enterotoxin
Keywordsstructural genomics / unknown function / all beta / SH3 / EntD / CPF_0587 / CPE0606 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process
Similarity search - Function
: / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / SH3 Domains ...: / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / SH3 Domains / SH3 type barrels. / SH3-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Probable enterotoxin
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Maglaqui, M. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Ramelot, T.A. / Cort, J.R. / Maglaqui, M. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / 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 SH3 domain from CPF_0587 (fragment 415-479) from Clostridium perfringens. Northeast Structural Genomics Consortium (NESG) Target CpR74A.
Authors: Ramelot, T.A. / Cort, J.R. / Maglaqui, M. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionDec 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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
Revision 1.4May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Probable enterotoxin


Theoretical massNumber of molelcules
Total (without water)8,3041
Polymers8,3041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Probable enterotoxin


Mass: 8304.316 Da / Num. of mol.: 1 / Fragment: SH3 domain, residues 497-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Species: perfringens / Gene: CPE0606, CPF_0587, entD / Plasmid: pET21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q8XMT2

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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 1H-15N NOESY
1413D 1H-13C NOESY aliph
1513D HNCO
1613D HN(CO)CA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11223D (H)CCH-TOCSY
11324D (H)CCH NOESY
11413D 1H-13C NOESY arom

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
220 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 0.8 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
320 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 0.9 mM [U-5% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMES1
100 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
0.8 mMprotein[U-100% 13C; U-100% 15N]1
20 mMMES2
100 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
0.8 mMprotein[U-100% 13C; U-100% 15N]2
20 mMMES3
100 mMsodium chloride3
5 mMcalcium chloride3
10 mMDTT3
0.02 %sodium azide3
0.9 mMprotein[U-5% 13C; U-100% 15N]3
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 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 NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5(PDBStat) R. Tejero, G.T. Montelionedata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: NIH-Xplor hbdb refinement
NMR constraintsNOE constraints total: 939 / NOE intraresidue total count: 194 / NOE long range total count: 438 / NOE medium range total count: 88 / NOE sequential total count: 219 / Hydrogen bond constraints total count: 2 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 52 / Protein psi angle constraints total count: 52
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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