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- PDB-6dnw: Sequence Requirements of the Listeria innocua prophage attP site -

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Basic information

Entry
Database: PDB / ID: 6dnw
TitleSequence Requirements of the Listeria innocua prophage attP site
Components
  • (DNA (26-MER)) x 2
  • Putative integrase [Bacteriophage A118]
KeywordsDNA BINDING PROTEIN / site-specific recombination / phage integrase / serine integrase / attachment site / integration / specificity
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding / metal ion binding
Similarity search - Function
Putative Large Serine Recombinase; Chain B, Domain 2 / Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Hect, E3 ligase catalytic domain fold / Recombinase, conserved site / Site-specific recombinases active site. ...Putative Large Serine Recombinase; Chain B, Domain 2 / Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Hect, E3 ligase catalytic domain fold / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Integrase [Bacteriophage A118]
Similarity search - Component
Biological speciesListeria innocua serovar 6a
Listeria innocua Clip11262 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.849 Å
AuthorsLi, H. / Sharp, R. / Rutherford, K. / Gupta, K. / Van Duyne, G.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director5R01GM10875104 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Serine Integrase attP Binding and Specificity.
Authors: Li, H. / Sharp, R. / Rutherford, K. / Gupta, K. / Van Duyne, G.D.
History
DepositionJun 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative integrase [Bacteriophage A118]
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9664
Polymers53,9013
Non-polymers651
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-45 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.291, 57.112, 167.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative integrase [Bacteriophage A118]


Mass: 37927.301 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Details: 133-341,417-452 [342-416 deleted]
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: int / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q928V6
#2: DNA chain DNA (26-MER)


Mass: 7908.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria innocua Clip11262 (bacteria)
#3: DNA chain DNA (26-MER)


Mass: 8065.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria innocua Clip11262 (bacteria)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were obtained by hanging drop vapor diffusion at 21oC in 100 mM Tris HCL pH 7.5, 200 mM ammonium sulfate, and 25% (w:v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.849→39.971 Å / Num. obs: 11185 / % possible obs: 94.1 % / Observed criterion σ(F): 1 / Redundancy: 3 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.9
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1082 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KIS

4kis


Resolution: 2.849→39.971 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 24.62
RfactorNum. reflection% reflectionSelection details
Rfree0.256 547 5.09 %Random
Rwork0.2194 ---
obs0.2213 10749 93.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.849→39.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 1060 1 9 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033178
X-RAY DIFFRACTIONf_angle_d0.5634499
X-RAY DIFFRACTIONf_dihedral_angle_d19.7371716
X-RAY DIFFRACTIONf_chiral_restr0.041488
X-RAY DIFFRACTIONf_plane_restr0.001386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8488-3.13530.36371270.33092308X-RAY DIFFRACTION88
3.1353-3.58880.2971440.2522554X-RAY DIFFRACTION95
3.5888-4.52050.18641350.20152625X-RAY DIFFRACTION97
4.5205-39.9750.26241410.18732715X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56150.07430.08950.0377-0.02330.10230.40330.20030.8901-0.1211-0.1714-0.68860.18210.7169-0.07850.43130.06890.15440.41780.0190.6041-1.16419.4049-19.6502
21.9976-2.02080.22216.8949-1.53865.90490.42580.6511-0.9331-0.5992-0.56480.1927-0.47690.03610.09140.4121-0.05070.03480.4642-0.05680.3542-6.8549-5.4983-12.5449
33.2683-0.65630.08024.36160.79663.84520.09670.0441-0.19380.3570.0093-0.10630.3825-0.3495-0.11420.2105-0.0407-0.0510.3470.03040.3665-7.6527-6.56682.034
44.5149-1.8231-4.30358.1046-1.47427.82580.3566-0.10010.6475-0.03270.184-0.2894-0.9177-0.6798-0.55760.35960.0937-0.05170.4834-0.06080.367-9.39987.4196-6.3441
57.15682.04491.51350.62170.13824.1596-0.0919-0.07670.83660.77490.1238-0.0348-0.603-0.11020.20280.54160.0283-0.14490.3348-0.08430.3848-1.61074.549912.4809
64.07461.2870.44285.3646-1.16725.39350.0493-0.36680.09470.409-0.26910.0652-0.1677-0.01890.25310.38350.0369-0.15340.2911-0.05690.42789.32275.409932.6396
73.4992-1.25560.64340.99521.48885.8734-0.01220.141.1812-0.0131-0.71811.1878-0.7442-0.95860.63270.73730.1722-0.20120.4889-0.21520.747-1.614911.068427.4834
84.2548-1.5383-0.84095.5093-6.27348.8912-0.0519-0.8251-0.0291.34940.3006-0.65340.3794-0.55210.22141.0892-0.0039-0.31270.58020.04040.467916.5458-1.195944.6422
96.13753.96744.21543.37242.15293.50280.26180.8804-0.49660.52050.7624-0.9102-1.11781.8325-1.02640.95160.0548-0.07230.8623-0.16580.601423.7328-3.320226.854
107.9713-4.84791.05979.21751.7187.59110.65770.5296-1.05070.7162-0.3521-0.16660.23090.0043-0.52520.3375-0.0149-0.09650.31510.00020.4868.973-4.63113.3145
112.8695-2.6995-3.3085.76275.80337.57130.64280.2950.7717-1.37610.7941-1.1824-1.3431.1941-1.59690.5238-0.08210.12710.6574-0.05110.534413.9287-0.3373-4.0047
124.0784-1.54171.2594.2914-1.68743.18060.8990.56170.4232-1.3466-0.518-0.62070.25721.158-0.28010.6610.12680.15640.6399-0.00840.40392.9342-0.7677-21.6712
132.72490.6807-0.15482.54212.25145.66440.55710.30840.3356-1.047-0.446-0.84070.08950.7144-0.14090.55370.21060.14080.58870.14980.5426.6919-0.1813-17.2962
141.1473-0.14870.54730.0227-0.06830.2795-0.1827-0.1179-0.00840.42661.1871-1.05090.37731.0136-1.0410.25950.0628-0.07630.7347-0.17720.602715.1933-4.26494.7746
153.3035-0.9446-0.99244.6907-4.06734.6080.5828-0.4617-0.5804-0.3124-0.4527-0.28311.0851.4340.26420.67290.0428-0.2470.40230.0940.47213.1016-1.991122.9459
161.96170.31322.20021.10661.42484.13930.0858-0.9296-0.32290.28870.217-0.35850.23350.53860.1530.90240.1624-0.96361.0734-0.01520.988324.0563-6.248337.629
178.56680.75833.24845.49170.97125.20040.0853-0.42320.0208-0.17810.60050.60350.4755-0.7543-0.64580.9397-0.094-0.42211.19360.2441.224322.95243.332746.1739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 134 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 163 )
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 243 )
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 264 )
6X-RAY DIFFRACTION6chain 'A' and (resid 265 through 425 )
7X-RAY DIFFRACTION7chain 'A' and (resid 426 through 452 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 5 )
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 10 )
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 15 )
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 20 )
12X-RAY DIFFRACTION12chain 'B' and (resid 21 through 26 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 10 )
14X-RAY DIFFRACTION14chain 'C' and (resid 11 through 15 )
15X-RAY DIFFRACTION15chain 'C' and (resid 16 through 20 )
16X-RAY DIFFRACTION16chain 'C' and (resid 21 through 25 )
17X-RAY DIFFRACTION17chain 'C' and (resid 26 through 26 )

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