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- PDB-1f44: CRYSTAL STRUCTURE OF TRIMERIC CRE RECOMBINASE-LOX COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1f44
TitleCRYSTAL STRUCTURE OF TRIMERIC CRE RECOMBINASE-LOX COMPLEX
Components
  • CRE RECOMBINASE
  • DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
  • DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
KeywordsHYDROLASE / LIGASE/DNA / SITE-SPECIFIC RECOMBINASE / RECOMBINATION / PROTEIN-DNA COMPLEX / TRIMERIC / THREE-WAY JUNCTION / BRANCHED DNA / Y-JUNCTION / 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 / Resolution: 2.05 Å
AuthorsBaldwin, E.P. / Woods, K.C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction.
Authors: Woods, K.C. / Martin, S.S. / Chu, V.C. / Baldwin, E.P.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 3, 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 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
N: DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
A: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)47,2773
Polymers47,2773
Non-polymers00
Water5,585310
1
M: DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
N: DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
A: CRE RECOMBINASE

M: DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
N: DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
A: CRE RECOMBINASE

M: DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
N: DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
A: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)141,8319
Polymers141,8319
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)160.653, 160.653, 160.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Cell settingcubic
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

DetailsTrimeric complex constructed from chains A, B and C by crystallographic three-fold.

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Components

#1: DNA chain DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')


Mass: 4872.190 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')


Mass: 5842.821 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein CRE RECOMBINASE / RECOMBINASE - PHAGE P1


Mass: 36561.844 Da / Num. of mol.: 1 / Mutation: Y324F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: CRE RECOMBINASE / Production host: Escherichia coli (E. coli) / References: UniProt: P06956
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 125 mM LI2SO4, 4% PEG 8000, 40mM NaPIPES PH 6.1, 5% MPD, VAPOR DIFFUSION, HANGING DROP at 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1LI2SO411
2NaPIPES11
3MPD11
4PEG 800011
5MPD12
6PEG 800012
Crystal grow
*PLUS
Temperature: 20-22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 %(w/v)PEG80001reservoir
2125 mM1reservoirLiSO4
320 mM1reservoirNa-PIPES
460 mM1reservoirNaCl
51
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 43161 / Num. obs: 42556 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 19.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.339 / Num. unique all: 5657 / % possible all: 99.9
Reflection shell
*PLUS
Rmerge(I) obs: 0.334

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementResolution: 2.05→5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2063 5.5 %random using CCP4 "unique" module
Rwork0.176 ---
all0.176 37741 --
obs0.176 37741 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.05→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 711 0 310 3537
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / σ(F): 0 / Rfactor all: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.25
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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