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- PDB-2key: Solution NMR structure of a domain from a putative phage integras... -

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Basic information

Entry
Database: PDB / ID: 2key
TitleSolution NMR structure of a domain from a putative phage integrase protein BF2284 from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR257C
ComponentsPutative phage integraseSite-specific recombination
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein structure / PSI / NESG / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
Phage integrase SAM-like domain / Arm, DNA-binding domain / Phage integrase SAM-like domain / 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 ...Phage integrase SAM-like domain / Arm, DNA-binding domain / Phage integrase SAM-like domain / 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
Putative phage integrase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Sathyamoorthy, B. / Sukumaran, D.K. / Lee, D. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Acton, T.B. / Swapna, G.V.T. / Rost, B. ...Mills, J.L. / Sathyamoorthy, B. / Sukumaran, D.K. / Lee, D. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Acton, T.B. / Swapna, G.V.T. / Rost, B. / Nair, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of a Domain from a Putative Phage Integrase Protein, BF2284, from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR257C
Authors: Mills, J.L. / Sathyamoorthy, B. / Sukumaran, D.K. / Lee, D. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Acton, T.B. / Swapna, G.V.T. / Rost, B. / Nair, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionFeb 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phage integrase


Theoretical massNumber of molelcules
Total (without water)13,4821
Polymers13,4821
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative phage integrase / Site-specific recombination


Mass: 13482.380 Da / Num. of mol.: 1 / Fragment: UNP residues 96-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2284 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5LD33

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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
1313D HNNCO
141(4,3)D GFT HNNCABCA
151(4,3)D GFT CABCA(CO)NHN
161(4,3)D GFT HabCab(CO)NHN
171(4,3)D GFT (H)CCH
1813D simultaneous NCaliCaro HH NOESY
1922D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.05 mM [U-99% 13C; U-99% 15N] BfR257C-1, 10 % [U-2H] D2O-2, 90 % H2O-3, 50 uM DSS-4, 10 mM DTT-5, 200 mM sodium chloride-6, 0.02 % sodium azide-7, 5 mM calcium chloride-8, 20 mM MES-9, 90% H2O/10% D2O90% H2O/10% D2O
20.77 mM [U-5% 13C; U-99% 15N] BfR257C-10, 10 % [U-2H] D2O-11, 90 % H2O-12, 50 uM DSS-13, 10 mM DTT-14, 200 mM sodium chloride-15, 0.02 % sodium azide-16, 5 mM calcium chloride-17, 20 mM MES-18, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.05 mMBfR257C-1[U-99% 13C; U-99% 15N]1
10 %D2O-2[U-2H]1
90 %H2O-31
50 uMDSS-41
10 mMDTT-51
200 mMsodium chloride-61
0.02 %sodium azide-71
5 mMcalcium chloride-81
20 mMMES-91
0.77 mMBfR257C-10[U-5% 13C; U-99% 15N]2
10 %D2O-11[U-2H]2
90 %H2O-122
50 uMDSS-132
10 mMDTT-142
200 mMsodium chloride-152
0.02 %sodium azide-162
5 mMcalcium chloride-172
20 mMMES-182
Sample conditionsIonic strength: 430 / pH: 6.5 / Pressure: ambient / Temperature: 298 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
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
SPSCANGlaserprocessing
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CSIWishart and Sykesstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PSVSBhattacharya and Montelionerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
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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