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- PDB-3crx: CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I -

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Basic information

Entry
Database: PDB / ID: 3crx
TitleCRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I
Components
  • (DNA 35-MER) x 4
  • 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: BNL / Processing site: NDB
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 1.3Nov 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 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
E: DNA 35-MER
F: DNA 35-MER
A: CRE RECOMBINASE
B: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)120,1706
Polymers120,1706
Non-polymers00
Water4,252236
1
C: DNA 35-MER
D: DNA 35-MER
E: DNA 35-MER
F: DNA 35-MER
A: CRE RECOMBINASE
B: CRE RECOMBINASE

C: DNA 35-MER
D: DNA 35-MER
E: DNA 35-MER
F: DNA 35-MER
A: CRE RECOMBINASE
B: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)240,34012
Polymers240,34012
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)106.300, 122.700, 179.500
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

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DNA chain , 4 types, 4 molecules CDEF

#1: DNA chain DNA 35-MER


Mass: 10758.980 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA 35-MER


Mass: 10718.956 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA 35-MER


Mass: 10758.980 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA 35-MER


Mass: 10799.004 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein / Non-polymers , 2 types, 238 molecules AB

#5: Protein CRE RECOMBINASE / CRE-HJ1 / RGBPP1 RECOMBINASE


Mass: 38567.152 Da / Num. of mol.: 2 / Mutation: R173K
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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE STRUCTURE REPRESENTED IN THIS ENTRY CONTAINS TWO CRE MOLECULES AND FOUR DNA STRANDS. THE DNA IN ...THE STRUCTURE REPRESENTED IN THIS ENTRY CONTAINS TWO CRE MOLECULES AND FOUR DNA STRANDS. THE DNA IN THIS STRUCTURE HAS TWO-FOLD DISORDER IN THE 4 BP REGIONS ADJACENT TO THE BRANCH POINTS IN EACH A ARM AND IN SINGLE BASE PAIR LOCATED WITHIN THE CRE BINDING SITE. THE OCCUPANCIES OF ATOMS THESE DISORDERED REGIONS HAVE BEEN SET TO 0.5.

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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: 2.41 Å3/Da / Density % sol: 50 %
Crystal growpH: 5 / Details: 50MM ACETATE PH 5.0, 26% MPD, 80MM MGCL2
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.065 MCre1drop
20.081 MloxS6 half-site1drop
325 mMsodium acetate1drop
412.5 %MPD1drop
55 mM1dropCaCl2
6120 mM1dropNaCl
72.5 mMdithiothreitol1drop
80.5 mMspermine1drop
950 mMsodium acetate1reservoir
1024 %MPD1reservoir
1120 mM1reservoirCaCl2
12200 mM1reservoirNaCl

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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: 2.7→48 Å / Num. obs: 38807 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 65.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 20
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.329 / % possible all: 93.2
Reflection
*PLUS
Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.329

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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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