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- PDB-2kyb: Solution structure of CpR82G from Clostridium perfringens. North ... -

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Basic information

Entry
Database: PDB / ID: 2kyb
TitleSolution structure of CpR82G from Clostridium perfringens. North East Structural Genomics Consortium Target CpR82g
ComponentsMannosyl-glycoprotein endo-beta-N-acetylglucosaminidase domain protein, possible enterotoxin
KeywordsTOXIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / SH3-like domain, bacterial-type / SH3 Domains / SH3 type barrels. / SH3-like domain superfamily ...Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / SH3-like domain, bacterial-type / SH3 Domains / SH3 type barrels. / SH3-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase domain protein, possible enterotoxin / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase domain protein, possible enterotoxin
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsMobley, C.K. / Lee, H. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everrett, J.K. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of CpR82G
Authors: Mobley, C.K. / Lee, H. / Montelione, G.T. / Prestegard, J.H.
History
DepositionMay 21, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_sample_details ...pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _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: Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase domain protein, possible enterotoxin


Theoretical massNumber of molelcules
Total (without water)6,3391
Polymers6,3391
Non-polymers00
Water00
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 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase domain protein, possible enterotoxin


Mass: 6339.147 Da / Num. of mol.: 1 / Fragment: sequence database residues 300-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124, NCTC 8237, Type A / Gene: entD, CPF_1439 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0TR56, UniProt: A0A0H2YV13*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D C(CO)NH
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1413D CBCA(CO)NH
1512D 1H-13C HSQC
1612D 1H-15N HSQC
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D H(CCO)NH
11013D HN(CA)CB
11122D 1H-13C HSQC CT 28ms delay
11222D 1H-13C HSQC CT 42ms delay
11322D 1H-13C HSQC CT 56ms delay
1143NH-J-modulation
1154NH-J-modulation
11613D HNCO
1171hbcbcgcdhdA
1181hbcbcgcdceheA
11912D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.01 mM [U-100% 13C; U-100% 15N] CpR82G-1, 0.02 % sodium azide-2, 100 mM DTT-3, 5 mM Calcium Chloride-4, 100 mM sodium chloride-5, 20 mM MES-6, 95% H2O/5% D2O95% H2O/5% D2O
20.98 mM U-5% 13C; U-100% 15N CpR82G-7, 0.02 % sodium azide-8, 100 mM DTT-9, 5 mM Calcium Chloride-10, 100 mM sodium chloride-11, 20 mM MES-12, 95% H2O/5% D2O95% H2O/5% D2O
30.67 mM [U-100% 13C; U-100% 15N] CpR82G-13, 0.016 % sodium azide-14, 81.73 mM DTT-15, 4.09 mM Calcium Chloride-16, 81.73 mM sodium chloride-17, 16.35 mM MES-18, 4 % C12E5 PEG-19, 1.25 % Hexanol-20, 82.88% H2O/17.12% D2O82.88% H2O/17.12% D2O
40.92 mM CpR82G-21, 0.018 % sodium azide-22, 91.67 mM DTT-23, 4.58 mM Calcium Chloride-24, 91.67 mM sodium chloride-25, 18.32 mM MES-26, 7 % Positively Charged Compressed Polyacrylamide Gel-27, 91.3% H2O/8.7% D2O91.3% H2O/8.7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.01 mMCpR82G-1[U-100% 13C; U-100% 15N]1
0.02 %sodium azide-21
100 mMDTT-31
5 mMCalcium Chloride-41
100 mMsodium chloride-51
20 mMMES-61
0.98 mMCpR82G-7U-5% 13C; U-100% 15N2
0.02 %sodium azide-82
100 mMDTT-92
5 mMCalcium Chloride-102
100 mMsodium chloride-112
20 mMMES-122
0.67 mMCpR82G-13[U-100% 13C; U-100% 15N]3
0.016 %sodium azide-143
81.73 mMDTT-153
4.09 mMCalcium Chloride-163
81.73 mMsodium chloride-173
16.35 mMMES-183
4 %C12E5 PEG-193
1.25 %Hexanol-203
0.92 mMCpR82G-214
0.018 %sodium azide-224
91.67 mMDTT-234
4.58 mMCalcium Chloride-244
91.67 mMsodium chloride-254
18.32 mMMES-264
7 %Positively Charged Compressed Polyacrylamide Gel-274
Sample conditionsIonic strength: 205 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1.5Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJ8.0.b17Johnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
PSVSBhattacharya and Montelionedata 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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