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- PDB-2a3v: Structural basis for broad DNA-specificity in integron recombination -

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Basic information

Entry
Database: PDB / ID: 2a3v
TitleStructural basis for broad DNA-specificity in integron recombination
Components
  • DNA (31-MER)
  • DNA (34-MER)
  • site-specific recombinase IntI4
KeywordsRECOMBINATION / Protein-DNA complex
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, integron-type / Phage integrase, N-terminal SAM-like domain / : / Integrase, SAM-like, N-terminal / Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. ...Integrase, integron-type / Phage integrase, N-terminal SAM-like domain / : / Integrase, SAM-like, N-terminal / Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / 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
: / DNA / DNA (> 10) / Integron integrase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMacDonald, D. / Demarre, G. / Bouvier, M. / Mazel, D. / Gopaul, D.N.
CitationJournal: Nature / Year: 2006
Title: Structural basis for broad DNA-specificity in integron recombination.
Authors: MacDonald, D. / Demarre, G. / Bouvier, M. / Mazel, D. / Gopaul, D.N.
History
DepositionJun 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (31-MER)
F: DNA (34-MER)
G: DNA (31-MER)
H: DNA (34-MER)
A: site-specific recombinase IntI4
B: site-specific recombinase IntI4
C: site-specific recombinase IntI4
D: site-specific recombinase IntI4


Theoretical massNumber of molelcules
Total (without water)201,0728
Polymers201,0728
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.900, 170.200, 209.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsaymmetric unit contains 1 biological assembly

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Components

#1: DNA chain DNA (31-MER)


Mass: 12332.916 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Sythetic construct
#2: DNA chain DNA (34-MER)


Mass: 13208.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Sythetic construct
#3: Protein
site-specific recombinase IntI4


Mass: 37497.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor str. N16961 (bacteria)
Species: Vibrio cholerae / Strain: O1 biovar eltor str. N16961 / Gene: intI4 / Plasmid: pDG022 (pET derived) / Production host: Escherichia coli (E. coli) / Strain (production host): BlI5 / References: GenBank: 9657688, UniProt: O68847*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.3 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 4000, Ammonium Acetate, CaCl2, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Ammonium Acetate11
3CaCl211
4MES11
5water11
6PEG 400012
7Ammonium Acetate12
8CaCl212

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.8→44.6 Å / Num. all: 63712 / Num. obs: 63712 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.078 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.33 / Num. unique all: 18833 / Rsym value: 0.462 / % possible all: 91.4

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Processing

Software
NameVersionClassification
XDSdata reduction
SnBphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.6 Å
Cross valid method: maximum likelihood target using amplitudes
σ(F): 1 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3211 -RANDOM
Rwork0.234 ---
all0.235 63712 --
obs0.235 63682 96.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10498 2568 0 170 13236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_improper_angle_d1.037

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