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- PDB-2ief: Structure of the cooperative Excisionase (Xis)-DNA complex reveal... -

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Basic information

Entry
Database: PDB / ID: 2ief
TitleStructure of the cooperative Excisionase (Xis)-DNA complex reveals a micronucleoprotein filament
Components
  • 15-mer DNA
  • 19-mer DNA
  • 34-mer DNA
  • Excisionase
KeywordsDNA BINDING PROTEIN/DNA / Excisionase / Recombination Directionality Factor / Site Specific Recombination / Micronucleoprotein Filament / 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 / MAD / Resolution: 2.601 Å
AuthorsAbbani, M.A. / Papagiannis, C.V. / Sam, M.D. / Cascio, D. / Johnson, R.C. / Clubb, R.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly.
Authors: Abbani, M.A. / Papagiannis, C.V. / Sam, M.D. / Cascio, D. / Johnson, R.C. / Clubb, R.T.
History
DepositionSep 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: 15-mer DNA
E: 19-mer DNA
F: 34-mer DNA
A: Excisionase
B: Excisionase
C: Excisionase


Theoretical massNumber of molelcules
Total (without water)41,2476
Polymers41,2476
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.655, 111.655, 76.268
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain 15-mer DNA


Mass: 4620.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: first strand, 5'-end
#2: DNA chain 19-mer DNA


Mass: 5840.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: first strand, 3'-end
#3: DNA chain 34-mer DNA


Mass: 10404.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: second strand
#4: Protein Excisionase / Xis


Mass: 6793.799 Da / Num. of mol.: 3 / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: Xis / Plasmid: pSBET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03699
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.27 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 30% PEG 4000, 0.2M Ammonium Acetate 0.1M Sodium Citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Ammonium Acetate11
3Sodium Citrate11
4PEG 400012
5Ammonium Acetate12
6Sodium Citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2005 / Details: mirrors
RadiationMonochromator: Double Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→93.25 Å / Num. all: 16295 / Num. obs: 16295 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 68.1 Å2 / Rsym value: 0.079 / Net I/σ(I): 24.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.13 / Rsym value: 0.451 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
SHELXmodel building
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.601→55.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 17.676 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.396 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24577 863 5 %RANDOM
Rwork0.19876 ---
obs0.20105 16295 99.92 %-
all-16295 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.651 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.298 Å0.538 Å
Refinement stepCycle: LAST / Resolution: 2.601→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 1385 0 39 2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212992
X-RAY DIFFRACTIONr_bond_other_d0.0020.021720
X-RAY DIFFRACTIONr_angle_refined_deg0.6532.534335
X-RAY DIFFRACTIONr_angle_other_deg0.70334176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9285161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22620.24781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.50115257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5581529
X-RAY DIFFRACTIONr_chiral_restr0.070.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
X-RAY DIFFRACTIONr_nbd_refined0.2020.2466
X-RAY DIFFRACTIONr_nbd_other0.2540.21894
X-RAY DIFFRACTIONr_nbtor_refined0.2230.21243
X-RAY DIFFRACTIONr_nbtor_other0.0820.21263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.95521016
X-RAY DIFFRACTIONr_mcbond_other0.7512316
X-RAY DIFFRACTIONr_mcangle_it1.78811331
X-RAY DIFFRACTIONr_scbond_it2.79922897
X-RAY DIFFRACTIONr_scangle_it3.91333003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 70 -
Rwork0.354 1161 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4714-0.539-1.89495.4013-0.0563.1191-0.0387-0.39250.05780.37370.135-0.3856-0.0096-0.0432-0.0963-0.07890.0761-0.0137-0.0751-0.0058-0.034523.8846.92889.8377
26.0323-3.3-1.4144.1177-0.89284.85940.0260.00570.2112-0.19680.0261-0.15670.01840.0213-0.052-0.05990.01770.0254-0.0514-0.0218-0.0853.371263.2513.0315
34.7026-1.31370.40196.9826-0.9823.3746-0.0513-0.02920.4578-0.0026-0.11870.1636-0.2963-0.32990.17-0.12720.008-0.0267-0.0467-0.00760.0055-12.6182.86623.585
44.8985-3.2493-0.94118.51961.65721.82730.14590.826-0.0022-0.4825-0.5570.878-0.1312-0.43960.4111-0.11660.0066-0.15310.0384-0.0294-0.0122-23.539278.645915.1837
510.941-8.42870.49057.78240.19660.46260.0154-0.0484-1.86660.3098-0.06191.15030.17280.35890.04650.00320.0041-0.0016-0.0780.09670.17769.325937.657612.2578
65.0641-3.7001-0.63984.16160.94130.44930.1420.1977-0.6832-0.076-0.31940.74190.0305-0.14620.1774-0.0724-0.0314-0.02560.02930.027-0.0757-3.915954.231413.5996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AD2 - 552 - 55
2X-RAY DIFFRACTION2BE2 - 512 - 51
3X-RAY DIFFRACTION3CF2 - 532 - 53
4X-RAY DIFFRACTION4DA1 - 151 - 15
5X-RAY DIFFRACTION5EB16 - 341 - 19
6X-RAY DIFFRACTION6FC35 - 681 - 34

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