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- PDB-2kj8: NMR structure of fragment 87-196 from the putative phage integras... -

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Basic information

Entry
Database: PDB / ID: 2kj8
TitleNMR structure of fragment 87-196 from the putative phage integrase IntS of E. coli: Northeast Structural Genomics Consortium target ER652A, PSI-2
ComponentsPutative prophage CPS-53 integrase
KeywordsDNA BINDING PROTEIN / integrase / intS / intC / yfdB / CPS-53 / DNA integration / DNA recombination / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Unknown Function
Function / homology
Function and homology information


provirus excision / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / sequence-specific DNA binding / symbiont entry into host cell / identical protein binding
Similarity search - Function
Phage integrase, N-terminal SAM-like domain / Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / Integrase, SAM-like, N-terminal / Tyrosine recombinase, N-terminal domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain ...Phage integrase, N-terminal SAM-like domain / Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / Integrase, SAM-like, N-terminal / Tyrosine recombinase, N-terminal domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / 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
Prophage integrase IntS
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsno criteria, model 1
AuthorsCort, J.R. / Ramelot, T.A. / Wang, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G. / Xiao, R. / Everett, J.K. ...Cort, J.R. / Ramelot, T.A. / Wang, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of fragment 87-196 from the putative phage integrase IntS of E. coli
Authors: Cort, J.R. / Montelione, G.T. / Kennedy, M.A.
History
DepositionMay 25, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative prophage CPS-53 integrase


Theoretical massNumber of molelcules
Total (without water)13,8541
Polymers13,8541
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)20 / 40low restraint violations and energies
RepresentativeModel #1no criteria

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Components

#1: Protein Putative prophage CPS-53 integrase


Mass: 13853.734 Da / Num. of mol.: 1 / Fragment: sequence database residues 87-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2349, intC, intS, JW2345, yfdB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P37326

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The construct comprises resiudes 87-196 of the 385-residue full length protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D (H)CCH-COSY
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D CBCA(CO)NH
1913D C(CO)NH
11013D HNHA
11112D 1H-15N HSQC
11212D 1H-13C HSQC
11324D 1H-13C-13C-1H HMQC-NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
195 % H2O, 5 % [U-2H] D2O, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 w/v sodium azide, 0.95 mM [biosynthetically directed 5%C; U-99% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
2100 % [U-2H] D2O, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 w/v sodium azide, 1.2 mM [U-99% 13C; U-99% 15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
95 %H2O-11
5 %D2O-2[U-2H]1
20 mMMES-31
200 mMsodium chloride-41
5 mMcalcium chloride-51
10 mMDTT-61
0.02 w/vsodium azide-71
0.95 mMprotein-8[biosynthetically directed 5%C; U-99% 15N]1
100 %D2O-9[U-2H]2
20 mMMES-102
200 mMsodium chloride-112
5 mMcalcium chloride-122
10 mMDTT-132
0.02 w/vsodium azide-142
1.2 mMprotein-15[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 215 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
FelixAccelrys Software Inc.processing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: final refinement with LJ and electrostatic potential conducted in explicit water
NMR representativeSelection criteria: no criteria
NMR ensembleConformer selection criteria: low restraint violations and energies
Conformers calculated total number: 40 / Conformers submitted total number: 20

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