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- PDB-9yup: Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 9yup
TitleCrystal structure of PprA S-F-S tetramer from Deinococcus radiodurans
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN / PprA / Deinococcus / Deinococcus radiodurans / D. radiodurans / DNA repair / Genome reassembly / self-assembly / protein filament
Function / homologycellular response to desiccation / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / damaged DNA binding / DNA repair / CITRATE ANION / DNA repair protein PprA
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsSzabla, R. / Junop, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2008R00075 Canada
CitationJournal: To Be Published
Title: Self-assembly of PprA from D.radiodurans
Authors: Szabla, R. / Junop, M.S.
History
DepositionOct 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein PprA
B: DNA repair protein PprA
C: DNA repair protein PprA
D: DNA repair protein PprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9787
Polymers134,4114
Non-polymers5673
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.679, 123.221, 139.288
Angle α, β, γ (deg.)90.000, 93.687, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
DNA repair protein PprA / Pleiotropic protein promoting DNA repair


Mass: 33602.750 Da / Num. of mol.: 4 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Details: 1-8 deletion of PprA from D.radiodurans with D180K/D184K mutation and N-terminal poly-His fusion tag separated by a TEV protease site
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: pprA, DR_A0346 / Plasmid: pMJ5671
Details (production host): pDEST-527-based expression plasmid
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32504
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. | Protein solution: 2.4 mg/mL PprA (73 ...Details: 1.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. | Protein solution: 2.4 mg/mL PprA (73 uM), 150mM KCl, 20mM Tris, pH 7.5 | Crystallization solution: 400 mM Lithium citrate, 20% (w/v) PEG 3350 | Well solution: 1.5 M Ammonium sulfate
Temp details: Temperature-controlled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2017 / Details: IMCA-CAT default optics (April 2017)
RadiationMonochromator: IMCA-CAT default optics (April 2017) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.068→92.207 Å / Num. obs: 105944 / % possible obs: 91.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 36.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.067 / Rrim(I) all: 0.223 / Net I/σ(I): 9.7
Reflection shellResolution: 2.068→2.409 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.775 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5298 / CC1/2: 0.588 / Rpim(I) all: 0.605 / Rrim(I) all: 1.936 / % possible all: 63.2

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Processing

Software
NameVersionClassification
JDirectordata collection
autoPROC20250717data processing
XDSJan 19, 2025 (BUILT 20250714)data reduction
Aimless0.8.2data scaling
PHASER2.0_5824phasing
PHENIX2.0_5824refinement
RefinementMethod to determine structure: SAD / Resolution: 2.07→41.65 Å / SU ML: 0.1821 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 4886 4.71 %
Rwork0.2107 98821 -
obs0.2119 103707 51.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.76 Å2
Refinement stepCycle: LAST / Resolution: 2.07→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8447 0 39 171 8657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00558626
X-RAY DIFFRACTIONf_angle_d0.786611670
X-RAY DIFFRACTIONf_chiral_restr0.04321277
X-RAY DIFFRACTIONf_plane_restr0.01061556
X-RAY DIFFRACTIONf_dihedral_angle_d14.87213115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.090.483950.485635X-RAY DIFFRACTION0.66
2.09-2.120.270560.436476X-RAY DIFFRACTION1.29
2.12-2.1400.3044123X-RAY DIFFRACTION1.88
2.14-2.170.142420.358126X-RAY DIFFRACTION1.93
2.17-2.20.2913110.3421184X-RAY DIFFRACTION3.03
2.2-2.230.3494200.3086341X-RAY DIFFRACTION5.43
2.23-2.260.2994220.366463X-RAY DIFFRACTION7.11
2.26-2.290.3528250.374475X-RAY DIFFRACTION7.59
2.29-2.330.3433360.3409745X-RAY DIFFRACTION11.7
2.33-2.370.3507560.3251068X-RAY DIFFRACTION16.59
2.37-2.410.3621580.31041218X-RAY DIFFRACTION19.33
2.41-2.450.3647740.30011605X-RAY DIFFRACTION25.19
2.45-2.50.31561040.30071960X-RAY DIFFRACTION30.44
2.5-2.550.3131360.29752360X-RAY DIFFRACTION37.52
2.55-2.610.32051470.3143134X-RAY DIFFRACTION48.61
2.61-2.660.35891340.3273132X-RAY DIFFRACTION53.73
2.67-2.730.37082440.32313734X-RAY DIFFRACTION59.41
2.73-2.810.30282320.29844689X-RAY DIFFRACTION73.74
2.81-2.890.32672380.2755205X-RAY DIFFRACTION80.36
2.89-2.980.30132380.27335758X-RAY DIFFRACTION90.34
2.98-3.090.25333160.26026401X-RAY DIFFRACTION98.55
3.09-3.210.28732670.26166352X-RAY DIFFRACTION99.97
3.21-3.360.23593040.23646431X-RAY DIFFRACTION99.94
3.36-3.540.24332950.21785800X-RAY DIFFRACTION90.27
3.54-3.760.26132480.1945762X-RAY DIFFRACTION89.82
3.76-4.050.22113110.17826183X-RAY DIFFRACTION96.84
4.05-4.450.17723180.15946371X-RAY DIFFRACTION99.88
4.45-5.10.18813200.15926401X-RAY DIFFRACTION99.87
5.1-6.420.19313360.18526365X-RAY DIFFRACTION99.97
6.42-41.650.20393830.16056324X-RAY DIFFRACTION99.7

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