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- PDB-1rh6: Bacteriophage Lambda Excisionase (Xis)-DNA Complex -

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Basic information

Entry
Database: PDB / ID: 1rh6
TitleBacteriophage Lambda Excisionase (Xis)-DNA Complex
Components
  • 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'
  • 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'
  • Excisionase
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / DNA architectural protein / 'winged'-helix protein / phage excision / site-specific DNA recombination / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


provirus excision / DNA recombination / DNA binding / identical protein binding
Similarity search - Function
Excisionase (Xis) protein / Excisionase-like / Excisionase-like superfamily / Excisionase-like protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Excisionase
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsSam, M.D. / Cascio, D. / Johnson, R.C. / Clubb, R.T.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the excisionase-DNA complex from bacteriophage lambda.
Authors: Sam, M.D. / Cascio, D. / Johnson, R.C. / Clubb, R.T.
History
DepositionNov 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Derived calculations
Revision 1.4Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_validate_close_contact / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'
D: 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'
A: Excisionase
B: Excisionase


Theoretical massNumber of molelcules
Total (without water)22,7654
Polymers22,7654
Non-polymers00
Water2,738152
1
C: 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'
D: 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'
B: Excisionase


Theoretical massNumber of molelcules
Total (without water)15,9713
Polymers15,9713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Excisionase


Theoretical massNumber of molelcules
Total (without water)6,7941
Polymers6,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.215, 72.691, 38.801
Angle α, β, γ (deg.)90.00, 104.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'


Mass: 4605.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'


Mass: 4571.015 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Excisionase


Mass: 6793.799 Da / Num. of mol.: 2 / Fragment: Xis DBD (residues 1-55) / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: xis / Plasmid: pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): RJ3386 (BL21-DE3) / References: UniProt: P03699
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NaOAc, imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaOAc11
2imidazole11
3H2O11
4NaOAc12
5imidazole12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 32190 / % possible obs: 93.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 93.1 % / Biso Wilson estimate: 24.125 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 19.8
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 95.8 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 8.2 / Num. unique all: 3280 / Rsym value: 0.152 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.618 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22553 1161 5 %RANDOM
Rwork0.19117 ---
all0.19293 ---
obs0.19293 21990 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.551 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å21.19 Å2
2---1.23 Å20 Å2
3----1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.108 Å0.11 Å
Luzzati d res low-20 Å
Luzzati sigma a-0.086 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 574 0 152 1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211598
X-RAY DIFFRACTIONr_bond_other_d0.0020.021173
X-RAY DIFFRACTIONr_angle_refined_deg2.5822.3972278
X-RAY DIFFRACTIONr_angle_other_deg1.20232752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021329
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02241
X-RAY DIFFRACTIONr_nbd_refined0.2230.2239
X-RAY DIFFRACTIONr_nbd_other0.250.21286
X-RAY DIFFRACTIONr_nbtor_other0.0920.2773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.420.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4711.5539
X-RAY DIFFRACTIONr_mcangle_it2.4642882
X-RAY DIFFRACTIONr_scbond_it3.10231059
X-RAY DIFFRACTIONr_scangle_it4.4924.51396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 78
Rwork0.23 1613

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