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- PDB-2crx: STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-... -

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Basic information

Entry
Database: PDB / ID: 2crx
TitleSTRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION
Components
  • DNA 35-MER
  • PROTEIN (CRE RECOMBINASE)
KeywordsHYDROLASE / LIGASE/DNA / CRE RECOMBINASE / HOLLIDAY JUNCTION / RECOMBINATION / RECOMBINASE-DNA COMPLEX / 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 / DIFFERENCE FOURIER / Resolution: 2.5 Å
AuthorsGopaul, D.N. / Guo, F. / Vanduyne, G.D.
Citation
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.
#1: Journal: Nature / Year: 1997
Title: Structure of Cre Recombinase Complexed with DNA in a Site-Specific Recombination Synapse
Authors: Guo, F. / Gopaul, D.N. / Van Duyne, G.D.
History
DepositionJun 19, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA 35-MER
D: DNA 35-MER
A: PROTEIN (CRE RECOMBINASE)
B: PROTEIN (CRE RECOMBINASE)


Theoretical massNumber of molelcules
Total (without water)98,7104
Polymers98,7104
Non-polymers00
Water6,503361
1
C: DNA 35-MER
D: DNA 35-MER
A: PROTEIN (CRE RECOMBINASE)
B: PROTEIN (CRE RECOMBINASE)

C: DNA 35-MER
D: DNA 35-MER
A: PROTEIN (CRE RECOMBINASE)
B: PROTEIN (CRE RECOMBINASE)


Theoretical massNumber of molelcules
Total (without water)197,4218
Polymers197,4218
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)106.900, 122.500, 180.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: DNA chain DNA 35-MER


Mass: 10759.968 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (CRE RECOMBINASE) / CRE-HJ2 / RGBPP1 RECOMBINASE


Mass: 38595.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06956
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.96 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: 50MM ACETATE BUFFER PH 5.0, 25% MPD, 200MM NACL, 20MM CACL2, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1ACETATE BUFFER11
2NACL11
3CACL211
4MPD11
5MPD12
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 Mprotein1drop
20.02 MHJ11drop
350 mMsodium acetate1drop
480 mM1dropMgCl2
52 mMdithiothreitol1drop
622 %MPD1drop
750 mMsodium acetate1reservoir
826 %MPD1reservoir
980 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→27.3 Å / Num. obs: 38807 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 2.83 % / Biso Wilson estimate: 65.5 Å2 / Rsym value: 0.053 / Net I/σ(I): 20
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5 / Rsym value: 0.248 / % possible all: 91
Reflection
*PLUS
Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.248

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1CRX

1crx


Resolution: 2.5→27.3 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1940 5 %RANDOM
Rwork0.198 ---
obs0.198 36470 94.4 %-
Displacement parametersBiso mean: 58.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4873 1405 0 361 6639
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.95
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.41.5
X-RAY DIFFRACTIONx_mcangle_it6.52
X-RAY DIFFRACTIONx_scbond_it6.62
X-RAY DIFFRACTIONx_scangle_it92.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.389 188 5 %
Rwork0.344 3426 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor obs: 0.344

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