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- PDB-5crx: ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATIO... -

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Basic information

Entry
Database: PDB / ID: 5crx
TitleASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE
Components
  • DNA (35-MER)
  • PROTEIN (BACTERIOPHAGE P1 CRE GENE)
KeywordsPROTEIN/DNA / CRE RECOMBINASE / DNA BENDING / SITE SPECIFIC RECOMBINATION / PROTEIN-DNA INTERACTION / PROTEIN-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 / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily ...Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGuo, F. / Gopaul, D.N. / Van Duyne, G.D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse.
Authors: Guo, F. / Gopaul, D.N. / Van Duyne, G.D.
#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: 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
DepositionApr 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Nov 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 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)
A: PROTEIN (BACTERIOPHAGE P1 CRE GENE)
B: PROTEIN (BACTERIOPHAGE P1 CRE GENE)


Theoretical massNumber of molelcules
Total (without water)98,6784
Polymers98,6784
Non-polymers00
Water5,657314
1
C: DNA (35-MER)
D: DNA (35-MER)
A: PROTEIN (BACTERIOPHAGE P1 CRE GENE)
B: PROTEIN (BACTERIOPHAGE P1 CRE GENE)

C: DNA (35-MER)
D: DNA (35-MER)
A: PROTEIN (BACTERIOPHAGE P1 CRE GENE)
B: PROTEIN (BACTERIOPHAGE P1 CRE GENE)


Theoretical massNumber of molelcules
Total (without water)197,3578
Polymers197,3578
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)107.100, 123.100, 180.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
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 (BACTERIOPHAGE P1 CRE GENE)


Mass: 38579.164 Da / Num. of mol.: 2 / Mutation: Y324F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: CRE / Plasmid: PET21A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASMIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06956
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.97 Å3/Da / Density % sol: 50 %
Crystal growpH: 5 / Details: pH 5.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.100 mMprotein1drop
20.075 mMloxS site1drop
350 mMsodium acetate1drop
424 %MPD1drop
520 mM1dropCaCl2
640 mM1dropNaCl
72 mMdithiothreitol1drop
8100 mMsodium acetate1reservoir
925 %MPD1reservoir
1020 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9188
DetectorType: ADSC / Detector: CCD / Date: Dec 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2.7→99 Å / Num. obs: 32242 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 63.4 Å2 / Rsym value: 0.069 / Net I/σ(I): 12.59
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 3.71 % / Mean I/σ(I) obs: 23.76 / Rsym value: 0.23 / % possible all: 93.9
Reflection
*PLUS
Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRX

1crx


Resolution: 2.7→48 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
Rfree0.304 1511 5 %RANDOM
Rwork0.227 ---
obs0.227 30977 96.1 %-
Displacement parametersBiso mean: 50.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 1354 0 314 6364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.26
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.11.5
X-RAY DIFFRACTIONx_mcangle_it62
X-RAY DIFFRACTIONx_scbond_it6.22
X-RAY DIFFRACTIONx_scangle_it8.42.5
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.437 167 5 %
Rwork0.337 3253 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLN.A.
X-RAY DIFFRACTION4N.A.N.A.
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 48 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1
X-RAY DIFFRACTIONx_mcbond_it4.11.5
X-RAY DIFFRACTIONx_scbond_it6.22
X-RAY DIFFRACTIONx_mcangle_it62
X-RAY DIFFRACTIONx_scangle_it8.42.5
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.437 / % reflection Rfree: 5 % / Rfactor Rwork: 0.337

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