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- PDB-4kis: Crystal Structure of a LSR-DNA Complex -

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Basic information

Entry
Database: PDB / ID: 4kis
TitleCrystal Structure of a LSR-DNA Complex
Components
  • (DNA (26-MER)) x 2
  • Putative integrase [Bacteriophage A118]
Keywordsrecombination/DNA / recombinase domain / zinc-ribbon domain / coiled-coil motif / recombination-DNA complex
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsRutherford, K. / Yuan, P. / Perry, K. / Van Duyne, G.D.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Attachment site recognition and regulation of directionality by the serine integrases.
Authors: Rutherford, K. / Yuan, P. / Perry, K. / Sharp, R. / Van Duyne, G.D.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative integrase [Bacteriophage A118]
E: DNA (26-MER)
F: DNA (26-MER)
B: Putative integrase [Bacteriophage A118]
G: DNA (26-MER)
H: DNA (26-MER)
C: Putative integrase [Bacteriophage A118]
I: DNA (26-MER)
J: DNA (26-MER)
D: Putative integrase [Bacteriophage A118]
K: DNA (26-MER)
L: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,18925
Polymers220,51612
Non-polymers67313
Water1448
1
A: Putative integrase [Bacteriophage A118]
E: DNA (26-MER)
F: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4459
Polymers55,1293
Non-polymers3166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-79 kcal/mol
Surface area26010 Å2
MethodPISA
2
B: Putative integrase [Bacteriophage A118]
G: DNA (26-MER)
H: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2756
Polymers55,1293
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-47 kcal/mol
Surface area24160 Å2
MethodPISA
3
C: Putative integrase [Bacteriophage A118]
I: DNA (26-MER)
J: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2345
Polymers55,1293
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-40 kcal/mol
Surface area24600 Å2
MethodPISA
4
D: Putative integrase [Bacteriophage A118]
K: DNA (26-MER)
L: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2345
Polymers55,1293
Non-polymers1052
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-64 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)290.750, 290.750, 290.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsAUTHORS STATE THAT THE STRUCTURE IS OF A MONOMER AND ITS BIOLOGICAL ASSEMBLY IS A MONOMER.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative integrase [Bacteriophage A118]


Mass: 39155.633 Da / Num. of mol.: 4 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: CLIP 11262 / Gene: int / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q928V6

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DNA chain , 2 types, 8 molecules EGIKFHJL

#2: DNA chain
DNA (26-MER)


Mass: 7908.068 Da / Num. of mol.: 4 / Fragment: attP left half site top strand / Source method: obtained synthetically / Details: attP half-site
#3: DNA chain
DNA (26-MER)


Mass: 8065.274 Da / Num. of mol.: 4 / Fragment: attP left half site bottom strand / Source method: obtained synthetically / Details: attP half-site

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Non-polymers , 3 types, 21 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, CaCl2, MPD, glycerol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.97921
SYNCHROTRONAPS 24-ID-E20.97921
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 25, 2012
ADSC QUANTUM 3152CCDMar 26, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si crystal 14.8 Bragg angleSINGLE WAVELENGTHMx-ray1
2Si crystal 14.8 Bragg angleSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 432015 / Num. obs: 432015 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 14.25
Reflection shellResolution: 3.15→3.2 Å / Rmerge(I) obs: 0.791 / % possible all: 66.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→49.86 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 3353 5% of reflections from native data set
Rwork0.236 --
all0.239 67072 -
obs0.239 65933 -
Refinement stepCycle: LAST / Resolution: 3.2→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10086 4240 13 8 14347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.99

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