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- PDB-1xns: Peptide trapped Holliday junction intermediate in Cre-loxP recomb... -

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Basic information

Entry
Database: PDB / ID: 1xns
TitlePeptide trapped Holliday junction intermediate in Cre-loxP recombination
Components
  • (loxP DNA) x 2
  • Recombinase CRE
KeywordsHydrolase / Ligase/DNA / CRE Recombinase / holliday junction / recombination / complex (recombinase-DNA) / peptide inhibitor / Ligase-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 / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, 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) / Recombinase cre
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGhosh, K. / Lau, C.K. / Guo, F. / Segall, A.M. / Van Duyne, G.D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination.
Authors: Ghosh, K. / Lau, C.K. / Guo, F. / Segall, A.M. / Van Duyne, G.D.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_close_contact
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2

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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
A: Recombinase CRE
B: Recombinase CRE


Theoretical massNumber of molelcules
Total (without water)94,3704
Polymers94,3704
Non-polymers00
Water5,332296
1
C: loxP DNA
D: loxP DNA
A: Recombinase CRE
B: Recombinase CRE

C: loxP DNA
D: loxP DNA
A: Recombinase CRE
B: Recombinase CRE


Theoretical massNumber of molelcules
Total (without water)188,7418
Polymers188,7418
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)106.078, 121.529, 177.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain loxP DNA


Mass: 10774.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: part of Holliday junction
#2: DNA chain loxP DNA


Mass: 10439.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: part of Holliday junction
#3: Protein Recombinase CRE


Mass: 36577.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: CRE / 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


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.04 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20 mM ACETATE BUFFER PH 5.0, 25% MPD, 20 mM CACL2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.8→47.67 Å / Num. all: 27586 / Num. obs: 26172 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rsym value: 0.062
Reflection shellResolution: 2.8→2.88 Å / Rsym value: 0.197

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRX

1crx


Resolution: 2.8→47.67 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 13.947 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26541 1386 5 %RANDOM
Rwork0.19627 ---
obs0.19965 26172 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.295 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 1411 0 296 6807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216761
X-RAY DIFFRACTIONr_bond_other_d0.0020.025541
X-RAY DIFFRACTIONr_angle_refined_deg1.7132.2149418
X-RAY DIFFRACTIONr_angle_other_deg1.964312889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815642
X-RAY DIFFRACTIONr_chiral_restr0.0790.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026520
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021164
X-RAY DIFFRACTIONr_nbd_refined0.2150.21703
X-RAY DIFFRACTIONr_nbd_other0.2530.26867
X-RAY DIFFRACTIONr_nbtor_other0.090.23658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.288
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.2296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.282
X-RAY DIFFRACTIONr_mcbond_it0.7351.53190
X-RAY DIFFRACTIONr_mcangle_it1.4125104
X-RAY DIFFRACTIONr_scbond_it2.08133571
X-RAY DIFFRACTIONr_scangle_it3.7964.54314
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 100 -
Rwork0.298 1707 -
obs--87.1 %

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