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- PDB-2kkp: Solution NMR structure of the phage integrase SAM-like Domain fro... -

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Basic information

Entry
Database: PDB / ID: 2kkp
TitleSolution NMR structure of the phage integrase SAM-like Domain from Moth 1796 from Moorella thermoacetica. Northeast Structural Genomics Consortium Target MtR39K (residues 64-171).
ComponentsPhage integrase
KeywordsDNA BINDING PROTEIN / SAM-like domain / alpha-helical bundle / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Unknown function
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
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 speciesMoorella thermoacetica ATCC 39073 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Wang, H. / Ciccosanti, C. / Jang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Ramelot, T.A. / Wang, H. / Ciccosanti, C. / Jang, M. / 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 phage integrase SAM-like Domain from Moth 1796 from Moorella thermoacetica. Northeast Structural Genomics Consortium Target MtR39K (residues 64-171).
Authors: Ramelot, T.A. / Wang, H. / Ciccosanti, C. / Jang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 26, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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

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Assembly

Deposited unit
A: Phage integrase


Theoretical massNumber of molelcules
Total (without water)13,6491
Polymers13,6491
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 / 150structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Phage integrase


Mass: 13648.683 Da / Num. of mol.: 1 / Fragment: SAM-like domain sequence database residues 64-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica ATCC 39073 (bacteria)
Gene: Moth 1796, Moth_1796 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q2RHJ2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: SAM is "sterile alpha motif" The phage integrase N-terminal SAM-like domain -Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein ...Details: SAM is "sterile alpha motif" The phage integrase N-terminal SAM-like domain -Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11334D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] Moth_1796, 20 mM MES, 200 mM potassium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM [U-5% 13C; U-99% 15N] Moth_1796, 20 mM MES, 200 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
3.9 mM [U-100% 13C; U-100% 15N] Moth_1796, 20 mM MES, 200 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMMoth_1796-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMpotassium chloride-31
1.1 mMMoth_1796-4[U-5% 13C; U-99% 15N]2
20 mMMES-52
200 mMpotassium chloride-62
.9 mMMoth_1796-7[U-100% 13C; U-100% 15N]3
20 mMMES-83
200 mMsodium chloride-93
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 AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVSBhattacharya and Montelionestructure solution
PdbStat5.1Roberto Tejero and Gaetano T. Montelionestructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Original NOE assgnments were done with CYANA. This NOE restraints list was refined using iterative cycles of XPLOR-NIH standalone, and XPLOR+HB and CNSw refinement.
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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