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- PDB-1kbu: CRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION -

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Basic information

Entry
Database: PDB / ID: 1kbu
TitleCRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION
Components
  • (LOXP) x 2
  • CRE RECOMBINASE
KeywordsHYDROLASE / LIGASE/DNA / SITE-SPECIFIC RECOMBINASE / HOLLIDAY JUNCTION COMPLEX / DNA-PROTEIN CO-CRYSTAL / INT RECOMBINASE MECHANISM / 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 / ISOMORPHOUS MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMartin, S.S. / Pulido, E. / Chu, V.C. / Lechner, T. / Baldwin, E.P.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The Order of Strand Exchanges in Cre-LoxP Recombination and its Basis Suggested by the Crystal Structure of a Cre-LoxP Holliday Junction Complex
Authors: Martin, S.S. / Pulido, E. / Chu, V.C. / Lechner, T.S. / Baldwin, E.P.
#1: Journal: Embo J. / Year: 1998
Title: Structure of the Holliday Junction Intermediate in Cre-loxP Site-Specific Recombination
Authors: Gopaul, D.N. / Guo, F. / van Duyne, G.D.
#2: Journal: 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
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: LOXP
D: LOXP
A: CRE RECOMBINASE
B: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)99,7594
Polymers99,7594
Non-polymers00
Water4,270237
1
C: LOXP
D: LOXP
A: CRE RECOMBINASE
B: CRE RECOMBINASE

C: LOXP
D: LOXP
A: CRE RECOMBINASE
B: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)199,5178
Polymers199,5178
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)107.170, 121.600, 179.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE BIOLOGICAL ASSEMBLY IS A CRE TETRAMER BOUND TO TWO LOXP SITES, GENERATED FROM THE ASYMMETRIC UNIT BY THE CRYSTALLOGRAPHIC TWO-FOLD AXIS PLUS TRANSLATIONS: x, -y+1, -z+1

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Components

#1: DNA chain LOXP


Mass: 10510.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: part of Holliday junction
#2: DNA chain LOXP


Mass: 10399.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: part of Holliday junction / References: GenBank: 215626
#3: Protein CRE RECOMBINASE / CRE SITE-SPECIFIC RECOMBINASE


Mass: 39424.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LYS86 AND LYS201 INTERACTIONS WITH THE SCISSILE BASE SUGGEST HOW STRAND EXCHANGE ORDER IS DETERMINED
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: CRE / Plasmid: pET28b(+) / 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.: 237 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: MPD, sodium acetate, calcium chloride, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium acetate11
3CaCl211
Crystal grow
*PLUS
Temperature: 21-25 ℃ / pH: 7 / Method: vapor diffusion / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135-45 mg/mlprotein1drop
217-30 %MPD1reservoir
312.5-100 mMsodium acetate1reservoirpH5.0-5.5
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2000
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→24.5 Å / Num. all: 53608 / Num. obs: 53320 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.037 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7169 / Rsym value: 0.287 / % possible all: 89.8
Reflection
*PLUS
Num. obs: 44903 / % possible obs: 89 % / Num. measured all: 161433 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
Rmerge(I) obs: 0.287

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Processing

Software
NameVersionClassification
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: ISOMORPHOUS MOLECULAR REPLACEMENT
Starting model: combination of 1CRX and 4CRX (see publication for details)

1crx

4crx


Resolution: 2.2→5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2682 -RANDOM
Rwork0.231 ---
all0.231 53233 --
obs0.231 53233 89 %-
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 57.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 1511 0 237 6837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.58
LS refinement shellResolution: 2.2→2.28 Å /
RfactorNum. reflection
Rfree0.39 220
Rwork0.38 -
Refinement
*PLUS
Lowest resolution: 5 Å / Num. reflection obs: 45726 / Num. reflection Rfree: 2441 / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.61

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