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- PDB-2l7k: Solution NMR Structure of protein CD1104.2 from Clostridium diffi... -

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Basic information

Entry
Database: PDB / ID: 2l7k
TitleSolution NMR Structure of protein CD1104.2 from Clostridium difficile, Northeast Structural Genomics Consortium Target CfR130
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologySporulation protein-like / Putative transposon-transfer assisting protein / Putative transposon-transfer assisting superfamily / Putative transposon-transfer assisting protein / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Putative conjugative transposon protein Tn1549-like, CTn4-Orf17
Function and homology information
Biological speciesClostridium difficile (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, H. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Pulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, H. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of CfR130 from Clostridium difficile, Northeast Structural Genomics Consortium Target CfR130
Authors: Pulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, H. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / ...Authors: Pulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, H. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Feb 29, 2012Group: Database references / Structure summary
Revision 1.4Aug 15, 2012Group: Structure summary
Revision 1.5Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.6May 15, 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

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)8,7511
Polymers8,7511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 8750.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD1104.2, CD1104B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q18AW3

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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 aliphatic
1312D 1H-13C HSQC aromatic
141(4,3)D GFT-HNCACBCA
151(4,3)D GFT-CBCACA(CO)NHN
1613D HNCO
1713D HN(CA)CO
1813D GFT (H)CCH-COSY-ali
1913D GFT (H)CCH-COSY-aro
11013D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
11113D (H)CCH-TOCSY-ali
11222D 1H-13C CT-HSQC aliphatic
1131(4,3)D GFT-HABCAB(CO)NHN
11432D 1H-15N J-MODULATED HSQC
11542D 1H-15N J-MODULATED HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.61 mM [U-100% 13C; U-100% 15N] CfR130, 20 mM MES, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
21.68 mM [U-5% 13C; U-100% 15N] CfR130, 20 mM MES, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
31.68 mM [U-5% 13C; U-100% 15N] CfR130, 20 mM MES, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 4 % PEG, 90% H2O/10% D2O90% H2O/10% D2O
41.68 mM [U-5% 13C; U-100% 15N] CfR130, 20 mM MES, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 13.2 mg/ml Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.61 mMCfR130-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
0.02 %sodium azide-41
5 mMcalcium chloride-51
10 mMDTT-61
50 uMDSS-71
1.68 mMCfR130-8[U-5% 13C; U-100% 15N]2
20 mMMES-92
100 mMsodium chloride-102
0.02 %sodium azide-112
5 mMcalcium chloride-122
10 mMDTT-132
50 uMDSS-142
1.68 mMCfR130-15[U-5% 13C; U-100% 15N]3
20 mMMES-163
100 mMsodium chloride-173
0.02 %sodium azide-183
5 mMcalcium chloride-193
10 mMDTT-203
50 uMDSS-213
4 %PEG-223
1.68 mMCfR130-23[U-5% 13C; U-100% 15N]4
20 mMMES-244
100 mMsodium chloride-254
0.02 %sodium azide-264
5 mMcalcium chloride-274
10 mMDTT-284
50 uMDSS-294
13.2 mg/mLPf1 phage-304
Sample conditionsIonic strength: 0.11 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoStructure2.1Huang, Tejero, Powers and Montelionestructure solution
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CARA1.8.4Keller and Wuthrichdata analysis
PROSA6.4Guntertprocessing
PSVSBhattacharya and Montelioneanalysis of structure
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: energy minimization
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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