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- PDB-2hoi: Crystal structure of the tetrameric pre-cleavage synaptic complex... -

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Basic information

Entry
Database: PDB / ID: 2hoi
TitleCrystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination
Components
  • (LoxP DNA) x 2
  • Recombinase Cre
KeywordsRECOMBINATION/DNA / CRE-LOXP PRECLEAVAGE SYNAPSE / RECOMBINATION-DNA COMPLEX
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily ...Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / 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
DNA / DNA (> 10) / Recombinase cre
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsGhosh, K. / Van Duyne, G.D.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Synapsis of loxP sites by Cre recombinase.
Authors: Ghosh, K. / Guo, F. / Van Duyne, G.D.
History
DepositionJul 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: LoxP DNA
D: LoxP DNA
E: LoxP DNA
F: LoxP DNA
A: Recombinase Cre
B: Recombinase Cre
G: Recombinase Cre
H: Recombinase Cre


Theoretical massNumber of molelcules
Total (without water)197,1868
Polymers197,1868
Non-polymers00
Water14,808822
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.784, 136.784, 218.275
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: DNA chain LoxP DNA


Mass: 10703.945 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain LoxP DNA


Mass: 10815.003 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
Recombinase Cre


Mass: 38537.062 Da / Num. of mol.: 4 / Mutation: K201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06956
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MPD, SODIUM ACETATE, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2SODIUM ACETATE11
3CALCIUM CHLORIDE11
4H2O11
5SODIUM ACETATE12
6CALCIUM CHLORIDE12
7MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2003 / Details: MONOCHROMATOR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.601→19.92 Å / Num. all: 72945 / Num. obs: 59441 / % possible obs: 81.49 % / Rsym value: 0.09
Reflection shellHighest resolution: 2.601 Å / Rsym value: 0.198 / % possible all: 81.64

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRX

1crx


Resolution: 2.601→19.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / SU B: 8.873 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.791 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3007 5.1 %RANDOM
Rwork0.184 ---
all0.2227 72945 --
obs0.2227 59441 81.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.818 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.601→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10184 2805 0 822 13811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02113495
X-RAY DIFFRACTIONr_angle_refined_deg1.062.21718806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.62851284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02122.222504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.786151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.75715140
X-RAY DIFFRACTIONr_chiral_restr0.0620.22091
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029231
X-RAY DIFFRACTIONr_nbd_refined0.1740.26171
X-RAY DIFFRACTIONr_nbtor_refined0.2920.29008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.21027
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.213
X-RAY DIFFRACTIONr_mcbond_it0.3631.56575
X-RAY DIFFRACTIONr_mcangle_it0.648210212
X-RAY DIFFRACTIONr_scbond_it0.78138638
X-RAY DIFFRACTIONr_scangle_it1.3884.58594
LS refinement shellResolution: 2.601→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 220 -
Rwork0.236 4072 -
obs-4292 81.64 %

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