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- PDB-9om8: Crystal structure of PprA S-F filament from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 9om8
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 R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)119,1534
Polymers119,1534
Non-polymers00
Water00
1
A: DNA repair protein PprA

A: DNA repair protein PprA

A: DNA repair protein PprA

A: DNA repair protein PprA

D: DNA repair protein PprA

D: DNA repair protein PprA

D: DNA repair protein PprA

D: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

C: DNA repair protein PprA

C: DNA repair protein PprA

C: DNA repair protein PprA

C: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)476,61216
Polymers476,61216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation2_756-x+2,y,-z+11
crystal symmetry operation2_857-x+3,y,-z+21
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_666x+1,y+1,z+11
crystal symmetry operation2_766-x+2,y+1,-z+11
crystal symmetry operation2_867-x+3,y+1,-z+21
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation3_444x-1/2,y-1/2,z-11
crystal symmetry operation4_747-x+5/2,y-1/2,-z+21
crystal symmetry operation4_646-x+3/2,y-1/2,-z+11
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation3_454x-1/2,y+1/2,z-11
crystal symmetry operation4_757-x+5/2,y+1/2,-z+21
crystal symmetry operation4_656-x+3/2,y+1/2,-z+11
Unit cell
Length a, b, c (Å)298.840, 44.487, 89.751
Angle α, β, γ (deg.)90.000, 106.626, 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: 29788.281 Da / Num. of mol.: 4 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Details: 1-8 deletion
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Strain: R1 / Gene: pprA, DR_A0346 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32504
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: 2.24 Å3/Da / Density % sol: 47.7 % / Description: Flat rectangular prisms
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
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: 3.5 mg/mL PprA (117 ...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: 3.5 mg/mL PprA (117 uM), 150mM KCl, 20mM Tris, pH 7.5 | Crystallization solution: 0.2M LiCl, 20% (w/v) PEG 3350 | Well solution: 1.4 M (NH4)2SO4
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: APS / Beamline: 17-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.83→44 Å / Num. obs: 25122 / % possible obs: 90.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 26.14 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.073 / Rrim(I) all: 0.127 / Net I/σ(I): 7
Reflection shellResolution: 2.83→2.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1244 / CC1/2: 0.87 / Rpim(I) all: 0.194 / Rrim(I) all: 0.327 / % possible all: 90.7

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Processing

Software
NameVersionClassification
autoPROC1.05data processing
XDSbuild 20241002data reduction
Aimless0.7.15data scaling
PHENIX1.21.2_5419phasing
PHENIX1.21.2_5419model building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→39.86 Å / SU ML: 0.4139 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.7335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 1213 4.83 %
Rwork0.2126 23901 -
obs0.2155 25114 90.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.56 Å2
Refinement stepCycle: LAST / Resolution: 2.83→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 0 0 7449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957575
X-RAY DIFFRACTIONf_angle_d1.268710281
X-RAY DIFFRACTIONf_chiral_restr0.04721153
X-RAY DIFFRACTIONf_plane_restr0.01251367
X-RAY DIFFRACTIONf_dihedral_angle_d17.19612646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.950.38461340.26252694X-RAY DIFFRACTION92.66
2.95-3.080.32431600.24872661X-RAY DIFFRACTION93.81
3.08-3.240.3231650.24612663X-RAY DIFFRACTION93.12
3.24-3.440.3061430.24432684X-RAY DIFFRACTION92.08
3.44-3.710.25571170.19452641X-RAY DIFFRACTION90.9
3.71-4.080.24551150.1992627X-RAY DIFFRACTION89.52
4.08-4.670.25421210.18082636X-RAY DIFFRACTION90.9
4.67-5.880.23521170.19562669X-RAY DIFFRACTION89.58
5.88-39.860.2271410.19842626X-RAY DIFFRACTION85.9

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