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- PDB-1xo0: High resolution structure of the holliday junction intermediate i... -

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Basic information

Entry
Database: PDB / ID: 1xo0
TitleHigh resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination
Components
  • (loxP) x 2
  • Recombinase CRE
KeywordsHYDROLASE / LIGASE/DNA / CRE RECOMBINASE / HOLLIDAY JUNCTION / RECOMBINATION / COMPLEX (RECOMBINASE-DNA) / 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 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 1.3Oct 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 1.4Aug 23, 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
D: loxP
A: Recombinase CRE
B: Recombinase CRE


Theoretical massNumber of molelcules
Total (without water)94,6194
Polymers94,6194
Non-polymers00
Water8,881493
1
C: loxP
D: loxP
A: Recombinase CRE
B: Recombinase CRE

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


Theoretical massNumber of molelcules
Total (without water)189,2378
Polymers189,2378
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)107.400, 123.000, 180.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE IS A TETRAMER.

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Components

#1: DNA chain loxP


Mass: 10774.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PART OF HOLLIDAY JUNCTION
#2: DNA chain loxP


Mass: 10743.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PART OF HOLLIDAY JUNCTION
#3: Protein Recombinase CRE


Mass: 36549.832 Da / Num. of mol.: 2 / Mutation: R173K
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.: 493 / 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: 3.14 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20mM ACETATE BUFFER PH 5.0 40%MPD 20mM CACL2. , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9188 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2→26 Å / Num. all: 67741 / Num. obs: 58491 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.076
Reflection shellResolution: 2→2.09 Å / Num. unique all: 3025 / % possible all: 84.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRX

1crx


Resolution: 2→26 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The following bond distances are slightly long: peptide bond between chain B residues THR 202 and B LEU 203. phospho diester bridge between chain C nucleotides T 1 and A 2. phospho diester ...Details: The following bond distances are slightly long: peptide bond between chain B residues THR 202 and B LEU 203. phospho diester bridge between chain C nucleotides T 1 and A 2. phospho diester bridge between chain D nucleotides T 1 and A 2.
RfactorNum. reflectionSelection details
Rfree0.265 -RANDOM
Rwork0.219 --
all-67741 -
obs-58491 -
Refinement stepCycle: LAST / Resolution: 2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 1428 0 493 7017
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.1
LS refinement shellResolution: 2→2.09 Å

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