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- PDB-8vs5: Structure of catalytic domain of telomere resolvase, ResT, from B... -

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Basic information

Entry
Database: PDB / ID: 8vs5
TitleStructure of catalytic domain of telomere resolvase, ResT, from Borrelia garinii
ComponentsTelomere resolvase ResT
KeywordsDNA BINDING PROTEIN / Telomere resolvase / DNA-binding / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologyTelomere resolvase ResT / Telomere resolvase ResT superfamily / Telomere resolvase ResT/TelK catalytic domain / Telomere resolvase ResT
Function and homology information
Biological speciesBorreliella garinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.796 Å
AuthorsSemper, C. / Savchenko, A. / Watanabe, N. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structure analysis of the telomere resolvase from the Lyme disease spirochete Borrelia garinii reveals functional divergence of its C-terminal domain.
Authors: Semper, C. / Watanabe, N. / Karimullina, E. / Patel, D.T. / Di Leo, R. / Castellanos, M. / Patel, D.H. / Chaconas, G. / Savchenko, A.
History
DepositionJan 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomere resolvase ResT


Theoretical massNumber of molelcules
Total (without water)24,2191
Polymers24,2191
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.172, 85.172, 110.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Telomere resolvase ResT


Mass: 24219.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella garinii (bacteria) / Gene: BGAPBR_B0003 / Production host: Escherichia coli (E. coli) / References: UniProt: B8F151
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 4.08 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.5M ammonium sulfate, 0.1M Tris-HCl pH 8.5, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.796→50 Å / Num. obs: 18265 / % possible obs: 96.91 % / Redundancy: 23.6 % / Biso Wilson estimate: 42.71 Å2 / CC1/2: 0.643 / Net I/σ(I): 20.3
Reflection shellResolution: 2.796→2.85 Å / Num. unique obs: 10253 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.796→27.83 Å / SU ML: 0.2339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 1809 9.9 %
Rwork0.17 16456 -
obs0.1734 18265 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.1 Å2
Refinement stepCycle: LAST / Resolution: 2.796→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 0 52 1519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841495
X-RAY DIFFRACTIONf_angle_d0.94292014
X-RAY DIFFRACTIONf_chiral_restr0.051222
X-RAY DIFFRACTIONf_plane_restr0.0049254
X-RAY DIFFRACTIONf_dihedral_angle_d14.3088194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.2853830.2515790X-RAY DIFFRACTION59.07
2.87-2.960.26981200.2411126X-RAY DIFFRACTION83.74
2.96-3.050.24121360.23021281X-RAY DIFFRACTION96.46
3.05-3.160.28181500.21541336X-RAY DIFFRACTION99.6
3.16-3.290.25591470.18551317X-RAY DIFFRACTION99.93
3.29-3.440.21841480.18191322X-RAY DIFFRACTION100
3.44-3.620.21431410.15781305X-RAY DIFFRACTION100
3.62-3.840.19151420.14371343X-RAY DIFFRACTION100
3.84-4.140.15951570.12681332X-RAY DIFFRACTION100
4.14-4.550.14621460.11871315X-RAY DIFFRACTION100
4.55-5.210.14131460.12241324X-RAY DIFFRACTION100
5.21-6.550.20591470.19561340X-RAY DIFFRACTION99.93
6.55-27.830.24281460.21061325X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 25.4352947541 Å / Origin y: 10.940960963 Å / Origin z: 40.7779257465 Å
111213212223313233
T0.140727062419 Å2-0.0343671895265 Å20.0323612416833 Å2-0.229596652856 Å2-0.00903374660258 Å2--0.173038218085 Å2
L1.08778925858 °2-0.409604642489 °2-0.249206079965 °2-4.61679529216 °21.62893618374 °2--3.01628626253 °2
S-0.0899490804662 Å °0.305632354402 Å °-0.0438255174385 Å °-0.283437814214 Å °0.0999745659864 Å °-0.0964429457556 Å °-0.164679609179 Å °0.0698826480935 Å °0.029778915733 Å °
Refinement TLS groupSelection details: all

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