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- PDB-5hxy: Crystal structure of XerA recombinase -

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Basic information

Entry
Database: PDB / ID: 5hxy
TitleCrystal structure of XerA recombinase
ComponentsTyrosine recombinase XerA
KeywordsRECOMBINATION / recombinase / XerA
Function / homology
Function and homology information


tyrosine-based site-specific recombinase activity / DNA transposition / DNA binding / cytoplasm
Similarity search - Function
Tyrosine recombinase XerA / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / 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
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine recombinase XerA
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHwang, K.Y. / Nam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)NRF-2014R1A1A2059440 Korea, Republic Of
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)NRF-2014R1212513 Korea, Republic Of
CitationJournal: FEBS Lett. / Year: 2016
Title: Crystal structure of Thermoplasma acidophilum XerA recombinase shows large C-shape clamp conformation and cis-cleavage mode for nucleophilic tyrosine
Authors: Jo, C.H. / Kim, J. / Han, A.R. / Park, S.Y. / Hwang, K.Y. / Nam, K.H.
History
DepositionJan 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine recombinase XerA
B: Tyrosine recombinase XerA
C: Tyrosine recombinase XerA
D: Tyrosine recombinase XerA
E: Tyrosine recombinase XerA
F: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,70321
Polymers222,2786
Non-polymers1,42515
Water8,845491
1
A: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4265
Polymers37,0461
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3314
Polymers37,0461
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.860, 105.968, 115.586
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Tyrosine recombinase XerA / DNA recombinase


Mass: 37046.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Strain: DSM 1728 / Gene: xerA, Ta1314 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HIM5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, ADA, LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97952, 0.97987, 0.9800
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2008
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979521
20.979871
30.981
ReflectionResolution: 2.5→50 Å / Num. obs: 68638 / % possible obs: 95.4 % / Redundancy: 3.3 % / Net I/σ(I): 13.69

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.5→47.66 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.342 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.613 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24321 3479 5.1 %RANDOM
Rwork0.18847 ---
obs0.19129 65159 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.442 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å20.25 Å2
2---1.04 Å20 Å2
3---1.2 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13501 0 75 491 14067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913793
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213514
X-RAY DIFFRACTIONr_angle_refined_deg1.821.98918576
X-RAY DIFFRACTIONr_angle_other_deg0.862330990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17151642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93122.485648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.504152459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.94715148
X-RAY DIFFRACTIONr_chiral_restr0.120.22089
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023225
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2873.1566604
X-RAY DIFFRACTIONr_mcbond_other2.2873.1566603
X-RAY DIFFRACTIONr_mcangle_it3.674.7198234
X-RAY DIFFRACTIONr_mcangle_other3.674.7198235
X-RAY DIFFRACTIONr_scbond_it2.7853.5047189
X-RAY DIFFRACTIONr_scbond_other2.7113.4797130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3055.08110253
X-RAY DIFFRACTIONr_long_range_B_refined6.525.11816741
X-RAY DIFFRACTIONr_long_range_B_other6.36825.09516658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 220 -
Rwork0.267 4228 -
obs--83.88 %

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