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- PDB-8vj1: Structure of C-terminal domain of telomere resolvase, ResT, from ... -

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Basic information

Entry
Database: PDB / ID: 8vj1
TitleStructure of C-terminal 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: 2.26 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 5, 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
B: Telomere resolvase ResT
C: Telomere resolvase ResT


Theoretical massNumber of molelcules
Total (without water)28,0093
Polymers28,0093
Non-polymers00
Water91951
1
A: Telomere resolvase ResT


Theoretical massNumber of molelcules
Total (without water)9,3361
Polymers9,3361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomere resolvase ResT


Theoretical massNumber of molelcules
Total (without water)9,3361
Polymers9,3361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Telomere resolvase ResT


Theoretical massNumber of molelcules
Total (without water)9,3361
Polymers9,3361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.583, 114.583, 114.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11C-110-

HOH

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Components

#1: Protein Telomere resolvase ResT


Mass: 9336.498 Da / Num. of mol.: 3
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.: 51 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.8M sodium citrate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 12747 / % possible obs: 99.89 % / Redundancy: 104.8 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.902 / Net I/σ(I): 28.7
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 628 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→40.51 Å / SU ML: 0.2739 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.6773 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2465 1991 10.1 %
Rwork0.1876 17719 -
obs0.1935 11356 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.33 Å2
Refinement stepCycle: LAST / Resolution: 2.26→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 0 51 1923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771896
X-RAY DIFFRACTIONf_angle_d0.8542551
X-RAY DIFFRACTIONf_chiral_restr0.0432311
X-RAY DIFFRACTIONf_plane_restr0.0042302
X-RAY DIFFRACTIONf_dihedral_angle_d2.75051163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.310.382830.201635X-RAY DIFFRACTION2.28
2.31-2.380.3015580.2181519X-RAY DIFFRACTION35.82
2.38-2.450.28091360.19681189X-RAY DIFFRACTION80.94
2.45-2.530.24421610.20171457X-RAY DIFFRACTION99.32
2.53-2.620.29121680.20521452X-RAY DIFFRACTION100
2.62-2.720.23451680.20241460X-RAY DIFFRACTION100
2.72-2.850.30241620.1931474X-RAY DIFFRACTION100
2.85-30.23491690.17991459X-RAY DIFFRACTION99.88
3-3.180.24081650.1921469X-RAY DIFFRACTION99.94
3.18-3.430.2311690.18461452X-RAY DIFFRACTION99.75
3.43-3.770.23751660.1651446X-RAY DIFFRACTION99.51
3.77-4.320.2441560.16881471X-RAY DIFFRACTION99.57
4.32-5.440.21341620.16731445X-RAY DIFFRACTION98.47
5.44-40.510.26431480.23021391X-RAY DIFFRACTION93.78

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