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- PDB-6neo: Crystal structure of PprA filament from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 6neo
TitleCrystal structure of PprA filament from Deinococcus radiodurans
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN / PROTEIN FIBRIL / DNA damage repair / Radiation induced / Genome segregation / Filament formation
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 / MOLECULAR REPLACEMENT / Resolution: 5.94 Å
AuthorsSzabla, R. / Junop, M.S. / Rok, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2008R00075 Canada
CitationJournal: To Be Published
Title: Crystal structure of PprA filament from Deinococcus radiodurans
Authors: Szabla, R. / Junop, M.S. / Rok, M.
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)29,9191
Polymers29,9191
Non-polymers00
Water00
1
B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA

B: DNA repair protein PprA


  • defined by author
  • Evidence: gel filtration, Purified PprA elutes from a gel filtration column at a broad distribution of retention volumes. The retention volume corresponds to an oligomeric size ranging from a ...Evidence: gel filtration, Purified PprA elutes from a gel filtration column at a broad distribution of retention volumes. The retention volume corresponds to an oligomeric size ranging from a tetramer to a 50-mer and larger., scanning transmission electron microscopy, In vitro, PprA exists as a long filament of varying length, as observed by TEM. This behavior is independent of Deinococcus species of origin., microscopy, In vivo, PprA forms a thin strand spanning the septum of dividing D. radiodurans cells. This was visualized by fluorescence microscopy., The repeating filament assembly present in the crystal has been observed in other crystal forms, despite different symmetries and crystal packing., Residues that are required for DNA binding all map to two distinct faces of this assembly.
  • 359 kDa, 12 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)359,03412
Polymers359,03412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_553x,y,z-21
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation4_664-x+1,-y+1,z-11
crystal symmetry operation4_663-x+1,-y+1,z-21
crystal symmetry operation7_554y,x,-z-2/31
crystal symmetry operation7_553y,x,-z-5/31
crystal symmetry operation7_552y,x,-z-8/31
crystal symmetry operation10_664-y+1,-x+1,-z-2/31
crystal symmetry operation10_663-y+1,-x+1,-z-5/31
crystal symmetry operation10_662-y+1,-x+1,-z-8/31
Unit cell
Length a, b, c (Å)148.979, 148.979, 79.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 29919.477 Da / Num. of mol.: 1 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: pprA, DR_A0346 / Plasmid: pDEST-527
Details (production host): Gateway destination vector with TEV-protease cleavable N-terminal His tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32504

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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: 4.55 Å3/Da / Density % sol: 72.96 % / Description: long hexagonal-base prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine ...Details: 1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine trihydrochloride, 1,4-diaminobutane dihydrochloride, DL-ornithine monohydrochloride), 50% v/v Precipitant Mix 6 (25% w/v PEG4000, 40% w/v 1,2,6-hexanetriol), 0.1 M Buffer System 4 (Gly-Gly, AMPD) at pH 6.5. The drop was suspended over a 1.5 M ammonium sulfate dehydrating solution and incubated at 20 degrees C for about 5 months.
Temp details: Temperature-controlled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen gas cryostream / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 5.94→67.53 Å / Num. obs: 1513 / % possible obs: 98.8 % / Redundancy: 13.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.074 / Rrim(I) all: 0.278 / Χ2: 0.97 / Net I/σ(I): 9.5
Reflection shellResolution: 5.94→6.64 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 402 / CC1/2: 0.496 / Rpim(I) all: 0.565 / Χ2: 0.92 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER1.13_2998phasing
StructureStudio2.4data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MC8 chain B

6mc8


Resolution: 5.94→50.0319 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.03
RfactorNum. reflection% reflection
Rfree0.3088 74 4.93 %
Rwork0.2871 --
obs0.2881 1502 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.94→50.0319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 0 0 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011489
X-RAY DIFFRACTIONf_angle_d0.3572056
X-RAY DIFFRACTIONf_dihedral_angle_d7.704864
X-RAY DIFFRACTIONf_chiral_restr0.036248
X-RAY DIFFRACTIONf_plane_restr0.002294
LS refinement shellHighest resolution: 5.9395 Å

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