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- PDB-1m6x: Flpe-Holliday Junction Complex -

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Basic information

Entry
Database: PDB / ID: 1m6x
TitleFlpe-Holliday Junction Complex
Components
  • (Flp recombinase) x 2
  • (Symmetrized FRT site) x 3
KeywordsLIGASE / LYASE/DNA / TYROSINE RECOMBINASE / PROTEIN-DNA COMPLEX / HOLLIDAY-JUNCTION / DOMAIN-SWAPPING / LYASE-DNA COMPLEX
Function / homology
Function and homology information


plasmid recombination / site-specific recombinase activity / DNA binding, bending / single-stranded DNA binding / double-stranded DNA binding
Similarity search - Function
FLP Recombinase, lambda integrase-like, N-terminal domain (domain 1) / Recombinase Flp protein, C-terminal / Recombinase Flp protein, N-terminal / Recombinase Flp protein N-terminus / Recombinase Flp protein / Flp-type tyrosine recombinase domain profile. / Intergrase catalytic core / hpI Integrase; Chain A / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core ...FLP Recombinase, lambda integrase-like, N-terminal domain (domain 1) / Recombinase Flp protein, C-terminal / Recombinase Flp protein, N-terminal / Recombinase Flp protein N-terminus / Recombinase Flp protein / Flp-type tyrosine recombinase domain profile. / Intergrase catalytic core / hpI Integrase; Chain A / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Site-specific recombinase Flp
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsConway, A.B. / Chen, Y. / Rice, P.A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural Plasticity of the Flp-Holliday Junction Complex
Authors: Conway, A.B. / Chen, Y. / Rice, P.A.
History
DepositionJul 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Symmetrized FRT site
I: Symmetrized FRT site
F: Symmetrized FRT site
J: Symmetrized FRT site
G: Symmetrized FRT site
H: Symmetrized FRT site
A: Flp recombinase
B: Flp recombinase
C: Flp recombinase
D: Flp recombinase


Theoretical massNumber of molelcules
Total (without water)235,24710
Polymers235,24710
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.779, 116.511, 142.425
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the tetramer found within the asymmetric unit

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Components

#1: DNA chain Symmetrized FRT site


Mass: 3916.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 13-mer
#2: DNA chain Symmetrized FRT site


Mass: 6165.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 20-mer
#3: DNA chain Symmetrized FRT site


Mass: 10126.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 33-mer
#4: Protein Flp recombinase


Mass: 48667.711 Da / Num. of mol.: 2 / Fragment: Flpe / Mutation: P2S, L33S, Y108N, S294P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FLP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03870
#5: Protein Flp recombinase


Mass: 48747.691 Da / Num. of mol.: 2 / Fragment: Flpe / Mutation: P2S, L33S, Y108N, S294P
Source method: isolated from a genetically manipulated source
Details: modified tyr343
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FLP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03870
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 5Kmme, sodium cloride, calcium cloride, HEPES, xylitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein1drop
2100 mM1dropNaCl
310 mMHEPES1droppH7.0
42 mMdithiothreitol1drop
513 %(w/v)PEG5000 MME1reservoir
620 mMHEPES1reservoirpH7.0
7100 mM1reservoirNaCl
810 mM1reservoirCaCl2
920 %(w/v)xylitol1reservoir
102 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→37.5 Å / Num. all: 48174 / Num. obs: 48174 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.2 Å2
Reflection shellResolution: 2.8→3 Å / % possible all: 18.3
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLO

1flo


Resolution: 2.8→37.47 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 101588.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 4855 10.1 %RANDOM
Rwork0.239 ---
obs0.239 48174 75.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.9284 Å2 / ksol: 0.282775 e/Å3
Displacement parametersBiso mean: 61.3 Å2
Baniso -1Baniso -2Baniso -3
1--12.91 Å20 Å25.29 Å2
2--14.88 Å20 Å2
3----1.97 Å2
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.74 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13036 2617 0 0 15653
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.882
X-RAY DIFFRACTIONc_scangle_it3.692.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 193 10 %
Rwork0.401 1744 -
obs--18.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP_NOPUCKERS.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 500 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.324
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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