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- PDB-5jk0: Crystal structure of XerH site-specific recombinase bound to difH... -

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Basic information

Entry
Database: PDB / ID: 5jk0
TitleCrystal structure of XerH site-specific recombinase bound to difH substrate: pre-cleavage complex
Components
  • (DNA (30-MER)) x 2
  • Tyrosine recombinase XerH
KeywordsCELL CYCLE / Xer / tyrosine recombinase / site-specific recombinase / chromosome dimer resolution
Function / homology
Function and homology information


tyrosine-based site-specific recombinase activity / chromosome segregation / DNA recombination / cell division / DNA binding / cytoplasm
Similarity search - Function
Tyrosine recombinase XerH / Xer recombinase, N-terminal / Phage integrase SAM-like domain / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Tyrosine recombinase XerH
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Helicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBebel, A. / Barabas, O.
CitationJournal: Elife / Year: 2016
Title: Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.
Authors: Bebel, A. / Karaca, E. / Kumar, B. / Stark, W.M. / Barabas, O.
History
DepositionApr 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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
A: Tyrosine recombinase XerH
B: Tyrosine recombinase XerH
C: Tyrosine recombinase XerH
D: Tyrosine recombinase XerH
E: DNA (30-MER)
F: DNA (30-MER)
G: DNA (30-MER)
H: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,84420
Polymers204,9328
Non-polymers91212
Water20,4651136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38680 Å2
ΔGint-243 kcal/mol
Surface area70180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.280, 153.200, 169.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tyrosine recombinase XerH


Mass: 42000.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: xerH, HP_0675 / Plasmid: pETM-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25386

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (30-MER)


Mass: 9195.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Helicobacter pylori 26695 (bacteria)
#3: DNA chain DNA (30-MER)


Mass: 9269.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Helicobacter pylori 26695 (bacteria)

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Non-polymers , 5 types, 1148 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1136 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion / Details: 0.2M sodium chloride, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.1→48.89 Å / Num. obs: 120659 / % possible obs: 99.87 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rsym value: 0.104 / Net I/σ(I): 12.53
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.25 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JJV

5jjv


Resolution: 2.1→48.89 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.26
RfactorNum. reflection% reflection
Rfree0.2233 5769 4.78 %
Rwork0.1913 --
obs0.1928 120653 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11015 2434 58 1136 14643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314006
X-RAY DIFFRACTIONf_angle_d0.53319408
X-RAY DIFFRACTIONf_dihedral_angle_d17.5845332
X-RAY DIFFRACTIONf_chiral_restr0.0232218
X-RAY DIFFRACTIONf_plane_restr0.0022033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.30471900.29053758X-RAY DIFFRACTION100
2.1239-2.14890.32291830.27613799X-RAY DIFFRACTION100
2.1489-2.17510.30071770.26643788X-RAY DIFFRACTION100
2.1751-2.20260.28961900.24963806X-RAY DIFFRACTION100
2.2026-2.23160.31720.24773785X-RAY DIFFRACTION100
2.2316-2.26210.27592140.24093820X-RAY DIFFRACTION100
2.2621-2.29450.24751860.23413735X-RAY DIFFRACTION100
2.2945-2.32870.25671690.23343849X-RAY DIFFRACTION100
2.3287-2.36510.27491840.23313795X-RAY DIFFRACTION100
2.3651-2.40390.27312000.24073794X-RAY DIFFRACTION100
2.4039-2.44530.28431900.23123772X-RAY DIFFRACTION100
2.4453-2.48980.27871870.22743823X-RAY DIFFRACTION100
2.4898-2.53770.27011740.22923838X-RAY DIFFRACTION100
2.5377-2.58950.26752040.21923762X-RAY DIFFRACTION100
2.5895-2.64580.23541920.22493828X-RAY DIFFRACTION100
2.6458-2.70730.2341860.22593796X-RAY DIFFRACTION100
2.7073-2.7750.25361720.2223833X-RAY DIFFRACTION100
2.775-2.850.24811930.22853814X-RAY DIFFRACTION100
2.85-2.93390.26591900.21563844X-RAY DIFFRACTION100
2.9339-3.02860.25991960.21133817X-RAY DIFFRACTION100
3.0286-3.13680.23611940.21183825X-RAY DIFFRACTION100
3.1368-3.26240.24012130.20153812X-RAY DIFFRACTION100
3.2624-3.41080.22261850.18853847X-RAY DIFFRACTION100
3.4108-3.59060.21022200.18073827X-RAY DIFFRACTION100
3.5906-3.81550.21582020.16583850X-RAY DIFFRACTION100
3.8155-4.10990.19872260.15553792X-RAY DIFFRACTION99
4.1099-4.52320.15582280.13853840X-RAY DIFFRACTION100
4.5232-5.17710.18531980.14323916X-RAY DIFFRACTION100
5.1771-6.52020.17421750.16253986X-RAY DIFFRACTION100
6.5202-48.90630.17351790.15054133X-RAY DIFFRACTION100

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