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- PDB-9yl4: Crystal structure of PprA S-F filament from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 9yl4
TitleCrystal structure of PprA S-F filament 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 / DNA repair protein PprA
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 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
E: DNA repair protein PprA
F: DNA repair protein PprA
G: DNA repair protein PprA
H: DNA repair protein PprA
I: DNA repair protein PprA
J: DNA repair protein PprA
K: DNA repair protein PprA
L: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)359,02612
Polymers359,02612
Non-polymers00
Water00
1
A: DNA repair protein PprA
B: DNA repair protein PprA
C: DNA repair protein PprA
D: DNA repair protein PprA
E: DNA repair protein PprA
F: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA
C: DNA repair protein PprA
D: DNA repair protein PprA
E: DNA repair protein PprA
F: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA
C: DNA repair protein PprA
D: DNA repair protein PprA
E: DNA repair protein PprA
F: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)538,53918
Polymers538,53918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
crystal symmetry operation2_454-x-1/2,-y,z-1/21
2
G: DNA repair protein PprA
H: DNA repair protein PprA
I: DNA repair protein PprA
J: DNA repair protein PprA
K: DNA repair protein PprA
L: DNA repair protein PprA

G: DNA repair protein PprA
H: DNA repair protein PprA
I: DNA repair protein PprA
J: DNA repair protein PprA
K: DNA repair protein PprA
L: DNA repair protein PprA

G: DNA repair protein PprA
H: DNA repair protein PprA
I: DNA repair protein PprA
J: DNA repair protein PprA
K: DNA repair protein PprA
L: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)538,53918
Polymers538,53918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Unit cell
Length a, b, c (Å)95.837, 111.339, 402.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 29918.809 Da / Num. of mol.: 12 / 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: pMJ5671
Details (production host): pDEST-527-based expression plasmid
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32504
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: 2.89 Å3/Da / Density % sol: 57.4 % / Description: cube-shaped crystal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 2.0 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: 6.4 mg/mL PprA (214 ...Details: 2.0 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: 6.4 mg/mL PprA (214 uM), 150mM KCl, 20mM Tris, pH 7.5 | Crystallization solution (Molecular Dimensions - MCSG2 #82): 200 mM NaCl, 20% (w/v) PEG 8000, 100 mM CAPS:NaOH, pH 10.5 | Well solution: 1.25 M Ammonium sulfate
PH range: 7.5-10.5 / 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: APS / Beamline: 17-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2016 / Details: IMCA-CAT default optics (Dec 2016)
RadiationMonochromator: IMCA-CAT default optics (Dec 2016) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.7→107.318 Å / Num. obs: 34323 / % possible obs: 92.6 % / Redundancy: 21.7 % / Biso Wilson estimate: 134.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.066 / Rrim(I) all: 0.311 / Net I/σ(I): 8.4
Reflection shellResolution: 3.704→4.069 Å / Redundancy: 20.3 % / Rmerge(I) obs: 3.411 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1716 / CC1/2: 0.627 / Rpim(I) all: 0.785 / Rrim(I) all: 3.583 / % possible all: 64.6

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Processing

Software
NameVersionClassification
JDirectordata collection
autoPROC20250717data processing
XDSJan 19, 2025 (BUILT 20250data reduction
Aimless0.8.2data scaling
PHASER2.0_5824phasing
PHENIX2.0_5824refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→40.57 Å / SU ML: 0.5473 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.6309
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 1588 4.64 %
Rwork0.2264 32671 -
obs0.2291 34259 73.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 146.08 Å2
Refinement stepCycle: LAST / Resolution: 3.7→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25067 0 0 0 25067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003525487
X-RAY DIFFRACTIONf_angle_d0.602534479
X-RAY DIFFRACTIONf_chiral_restr0.03873796
X-RAY DIFFRACTIONf_plane_restr0.01034596
X-RAY DIFFRACTIONf_dihedral_angle_d16.21259201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.820.262890.3367211X-RAY DIFFRACTION5.26
3.82-3.960.39300.3175608X-RAY DIFFRACTION15.27
3.96-4.120.3754610.32181301X-RAY DIFFRACTION32.42
4.12-4.310.37971390.24962334X-RAY DIFFRACTION58.84
4.31-4.530.32281580.23063566X-RAY DIFFRACTION88.48
4.53-4.820.28571740.22254032X-RAY DIFFRACTION98.92
4.82-5.190.28461900.21994023X-RAY DIFFRACTION99.93
5.19-5.710.31782140.25044047X-RAY DIFFRACTION100
5.71-6.530.31322080.24634093X-RAY DIFFRACTION100
6.53-8.220.28811980.23214144X-RAY DIFFRACTION100
8.22-40.570.22292070.20134312X-RAY DIFFRACTION99.74

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