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- PDB-9or6: Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 9or6
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 / SPERMIDINE / DNA repair protein PprA
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSzabla, R. / Junop, M.S. / Wood, K.
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
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8985
Polymers59,4622
Non-polymers4363
Water84747
1
A: DNA repair protein PprA
B: DNA repair protein PprA
hetero molecules

A: DNA repair protein PprA
B: DNA repair protein PprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,79610
Polymers118,9254
Non-polymers8716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)183.486, 34.083, 98.734
Angle α, β, γ (deg.)90.000, 98.337, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 29731.230 Da / Num. of mol.: 2 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Details: 1-8 deletion of PprA from D.radiodurans with D180K/D184K mutation
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: pprA, DR_A0346 / Plasmid: pMJ5666
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-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50 % / Description: long and thin hexagonal-based prisms
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 1.5 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: 5.0 mg/mL PprA (168 ...Details: 1.5 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: 5.0 mg/mL PprA (168 uM), 43bp dsDNA (101 uM), 150mM KCl, 20mM Tris, pH 7.5, 1 mM MgCl2. | Crystallization solution (Molecular Dimensions - Morpheus 2 #94): 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4 Diaminobutane dihydrochloride, 10 mM DL Ornithine monohydrochloride 0.1M Gly-Gly, AMPD, pH 8.5, 13% w/v PEG 4000, 21% w/v 1,2,6 Hexanetriol. | Well solution: 2.0 M Ammonium sulfate.
PH range: 7.5-8.5 / 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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2019 / Details: CMCF-ID optics setup
RadiationMonochromator: CMCF-ID default optics (Feb 2019) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→90.774 Å / Num. obs: 13352 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 51.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Net I/σ(I): 9.6
Reflection shellResolution: 2.904→2.954 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 633 / CC1/2: 0.756 / Rpim(I) all: 0.417 / Rrim(I) all: 0.61 / % possible all: 100

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Processing

Software
NameVersionClassification
MxDCdata collection
autoPROC1.0.5 (20200206)data processing
XDSJan 31, 2020 (BUILT 20200131)data reduction
Aimless0.7.4data scaling
PHENIX1.21.2_5419phasing
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→90.77 Å / SU ML: 0.4166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 650 4.87 %
Rwork0.2266 12700 -
obs0.2276 13350 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.11 Å2
Refinement stepCycle: LAST / Resolution: 2.9→90.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 30 47 4070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374086
X-RAY DIFFRACTIONf_angle_d0.64165519
X-RAY DIFFRACTIONf_chiral_restr0.0428611
X-RAY DIFFRACTIONf_plane_restr0.0063729
X-RAY DIFFRACTIONf_dihedral_angle_d17.15931470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.130.33081410.27562572X-RAY DIFFRACTION99.89
3.13-3.430.34131270.27532527X-RAY DIFFRACTION99.36
3.46-3.940.27381120.23162209X-RAY DIFFRACTION88.69
3.94-4.970.20131370.20532650X-RAY DIFFRACTION99.57
4.97-90.770.21251330.20462742X-RAY DIFFRACTION99.52

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