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- PDB-2kiw: Solution NMR structure of the domain N-terminal to the integrase ... -

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Basic information

Entry
Database: PDB / ID: 2kiw
TitleSolution NMR structure of the domain N-terminal to the integrase domain of SH1003 from Staphylococcus haemolyticus. Northeast Structural Genomics Consortium Target ShR105F (64-166).
ComponentsInt protein
KeywordsDNA BINDING PROTEIN / alpha / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
AP2-like integrase, N-terminal domain / Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / Tyrosine recombinase, N-terminal domain / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core ...AP2-like integrase, N-terminal domain / Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / Tyrosine recombinase, N-terminal domain / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStaphylococcus haemolyticus JCSC1435 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Belote, R.L. / Foote, E.L. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. ...Yang, Y. / Ramelot, T.A. / Belote, R.L. / Foote, E.L. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G. / 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 the domain N-terminal to the integrase domain of SH1003 from Staphylococcus haemolyticus. Northeast Structural Genomics Consortium Target ShR105F (64-166).
Authors: Yang, Y. / Ramelot, T.A. / Belote, R.L. / Foote, E.L. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelio, G.T. / Kennedy, M.A.
History
DepositionMay 12, 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 / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...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: Int protein


Theoretical massNumber of molelcules
Total (without water)13,1231
Polymers13,1231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Int protein


Mass: 13122.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus haemolyticus JCSC1435 (bacteria)
Gene: int, SH1003 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q4L7R3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: residues 64-166 of SH1003
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D HN(CO)CA
11113D HBHA(CO)NH
11213D H(CCO)NH
11313D C(CO)NH
11413D (H)CCH-TOCSY
11513D (H)CCH-COSY
11633D (H)CCH-TOCSY
11734D CC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.84 mM [U-100% 13C; U-100% 15N] SH1003, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.79 mM SH1003, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.84 mM [U-100% 13C; U-100% 15N] SH1003, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.84 mMSH1003[U-100% 13C; U-100% 15N]1
20 mMMES1
200 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
0.79 mMSH10032
20 mMMES2
200 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
0.84 mMSH1003[U-100% 13C; U-100% 15N]3
20 mMMES3
200 mMsodium chloride3
5 mMcalcium chloride3
10 mMDTT3
0.02 %sodium azide3
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 293 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
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure solution
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-nih-2.20 with HBDB
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 20

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