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- PDB-2khq: Solution NMR structure of a phage integrase SSP1947 fragment 59-1... -

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Basic information

Entry
Database: PDB / ID: 2khq
TitleSolution NMR structure of a phage integrase SSP1947 fragment 59-159 from Staphylococcus saprophyticus, Northeast Structural Genomics Consortium Target SyR103B
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / all-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 saprophyticus subsp. saprophyticus ATCC 15305 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Mills, J.L. / Hua, J. / Belote, R.L. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Eletsky, A. / Mills, J.L. / Hua, J. / Belote, R.L. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G.V.T. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of a phage integrase SSP1947 fragment 59-159 from Staphylococcus saprophyticus
Authors: Eletsky, A. / Mills, J.L. / Hua, J. / Belote, R. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G.V.T. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionApr 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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)13,5291
Polymers13,5291
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 Integrase /


Mass: 13529.219 Da / Num. of mol.: 1 / Fragment: residues 59-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (bacteria)
Strain: ATCC 15305 / DSM 20229 / Gene: SSP1947 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q49VW8

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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 aliphatic
1312D 1H-13C CT-HSQC aliphatic
1412D 1H-13C CT-HSQC aromatic
1513D 1H-15N,13C NOESY
1613D 1H-13C NOESY
1713D HNCO
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D HN(CA)CO
11113D HBHA(CO)NH
11213D (H)CCH-COSY aliphatic
11313D (H)CCH-TOCSY aliphatic
11413D (H)CCH-COSY aromatic
11512D 1H-15N LR-HSQC
11622D 1H-13C CT-HSQC methyl
11712D MEXICO
11812D CLEANEX

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Sample preparation

Details
Solution-IDContentsSolvent system
10.69 mM [U-100% 13C; U-100% 15N] syr103b_protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-5% 13C; U-100% 15N] syr103b_protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.69 mMsyr103b_protein-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
50 uMDSS-51
0.02 %sodium azide-61
0.6 mMsyr103b_protein-7[U-5% 13C; U-100% 15N]2
20 mMMES-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
50 uMDSS-112
0.02 %sodium azide-122
Sample conditionsIonic strength: 0.215 / 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
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.0.2Guntertprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
CSI2Wishart and Sykesdata analysis
TALOS2007.068.09.07Shen, Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure validation
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based on ...Details: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based on preliminary structures and CLEANEX/MEXICO data. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with OPLSX force field.
NMR constraintsNOE constraints total: 2177 / NOE intraresidue total count: 408 / NOE long range total count: 648 / NOE medium range total count: 622 / NOE sequential total count: 499 / Hydrogen bond constraints total count: 180 / Protein phi angle constraints total count: 59 / Protein psi angle constraints total count: 59
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.32 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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