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- PDB-2kj9: NMR structure of IntB phage-integrase-like protein fragment 90-19... -

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Basic information

Entry
Database: PDB / ID: 2kj9
TitleNMR structure of IntB phage-integrase-like protein fragment 90-199 from Erwinia carotova subsp. atroseptica: Northeast Structural Genomics Consortium target EwR217E
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / integrase / DNA_BRE_C superfamily / bacteriophage P4 integrase / intB / Integrase-like_cat-core_phage / PSI-2 / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell / DNA binding
Similarity search - Function
Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / 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 ...Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / 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 speciesPectobacterium atrosepticum (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. / Acton, T.B. / Xiao, R. ...Cort, J.R. / Ramelot, T.A. / Wang, D. / Ciccosanti, C. / 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: NMR structure of IntB phage-integrase-like protein fragment 90-199 from Erwinia carotova subsp. atroseptica
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 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Integrase


Theoretical massNumber of molelcules
Total (without water)13,9591
Polymers13,9591
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 / 40structures with low energies and few restraint violations
RepresentativeModel #1no criteria

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Components

#1: Protein Integrase /


Mass: 13959.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: ECA2889, intB, intB/ECA2889 / Variant: subsp. atroseptica / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q6D355

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: structure of fragment representing residues 90-199 of the full length protein (428 amino acids)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D C(CO)NH
11013D (H)CCH-TOCSY
11113D HNHA
11212D 1H-15N HSQC
11322D 1H-13C HSQC
11434D 1H-13C-13C-1H HMQC-NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 0.02 w/v sodium azide, 95 % H2O, 5 % [U-99% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [5% biosynthetically directed 13C; U-99% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 0.02 w/v sodium azide, 95 % H2O, 5 % [U-99% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
30.7 mM [U-99% 13C; U-99% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 0.02 w/v sodium azide, 100 % [U-99% 2H] D2O-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-99% 13C; U-99% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 w/vsodium azide-51
95 %H2O-61
5 %D2O-7[U-99% 2H]1
0.7 mMentity-8[5% biosynthetically directed 13C; U-99% 15N]2
20 mMMES-92
200 mMsodium chloride-102
5 mMcalcium chloride-112
0.02 w/vsodium azide-122
95 %H2O-132
5 %D2O-14[U-99% 2H]2
0.7 mMentity-15[U-99% 13C; U-99% 15N]3
20 mMMES-163
200 mMsodium chloride-173
5 mMcalcium chloride-183
0.02 w/vsodium azide-193
100 %D2O-20[U-99% 2H]3
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
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
FelixAccelrys Software Inc.processing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: no criteria
NMR ensembleConformer selection criteria: structures with low energies and few restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 20

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