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- PDB-1q3v: Crystal structure of a wild-type Cre recombinase-loxP synapse: ph... -

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Basic information

Entry
Database: PDB / ID: 1q3v
TitleCrystal structure of a wild-type Cre recombinase-loxP synapse: phosphotyrosine covalent intermediate
Components
  • (loxP DNA) x 3
  • Cre recombinase
KeywordsREPLICATION/DNA / Cre / recombinase / DNA / REPLICATION-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
IODIDE ION / DNA / DNA (> 10) / Recombinase cre
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsEnnifar, E. / Meyer, J.E.W. / Buchholz, F. / Stewart, A.F. / Suck, D.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation
Authors: Ennifar, E. / Meyer, J.E.W. / Buchholz, F. / Stewart, A.F. / Suck, D.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: loxP DNA
X: loxP DNA
D: loxP DNA
G: loxP DNA
Y: loxP DNA
H: loxP DNA
A: Cre recombinase
B: Cre recombinase
E: Cre recombinase
F: Cre recombinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,29619
Polymers201,87210
Non-polymers4249
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.938, 164.160, 194.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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DNA chain , 3 types, 6 molecules CGXYDH

#1: DNA chain loxP DNA


Mass: 4963.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: First strand of loxP site, 5'-end
#2: DNA chain loxP DNA


Mass: 6452.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: First strand of loxP site, 3'-end
#3: DNA chain loxP DNA


Mass: 11387.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Second strand of loxP site

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Protein , 1 types, 4 molecules ABEF

#4: Protein
Cre recombinase / GST-loxP-cre recombinase fusion protein / Retrofitting vector pRetroES


Mass: 39066.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Plasmid: pGem / Production host: Escherichia coli (E. coli) / References: UniProt: P06956

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Non-polymers , 3 types, 12 molecules

#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.68 Å3/Da / Density % sol: 73.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: NaCl, EDTA, Glycerol, HEPES, MgCl2, PEG 2000, MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MME11
2HEPES11
3NaCl11
4MgCl211
5EDTA11
6Glycerol11
7PEG 200011
8NaCl12
9MgCl212
10EDTA12
11Glycerol12
12PEG 200012
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51
61
71
81
91
101
111
121

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.91→30 Å / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 70.3 Å2 / Rsym value: 0.067
Reflection shellHighest resolution: 2.91 Å / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 2.9 Å / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.33

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Processing

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

1crx


Resolution: 2.91→29.92 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 3610 5.1 %RANDOM
Rwork0.247 ---
obs0.2471 70849 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.1226 Å2 / ksol: 0.285478 e/Å3
Displacement parametersBiso mean: 70.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.85 Å20 Å20 Å2
2--5.59 Å20 Å2
3----12.45 Å2
Refine analyzeLuzzati coordinate error free: 0.54 Å / Luzzati sigma a free: 0.64 Å
Refinement stepCycle: LAST / Resolution: 2.91→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10264 3020 9 3 13296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 2.91→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.539 519 5 %
Rwork0.512 9937 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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