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- PDB-6mc6: Crystal structure of PprA filament from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 6mc6
TitleCrystal structure of PprA filament from Deinococcus radiodurans
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN / DNA damage repair / Radiation induced / Genome segregation / Filment formation
Function / homology
Function and homology information


cellular 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
Similarity search - Function
: / : / PprA N-terminal domain / PprA second domain
Similarity search - Domain/homology
DNA repair protein PprA
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.747 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: Crystal structure of PprA from Deinococcus radiodurans
Authors: Szabla, R. / Wood, K. / Junop, M.S.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)59,8392
Polymers59,8392
Non-polymers00
Water79344
1
A: DNA repair protein PprA
B: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA

A: DNA repair protein PprA
B: DNA repair protein PprA

A: 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 this crystal has been observed in numerous 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.
  • 479 kDa, 16 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)478,71216
Polymers478,71216
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation2_565x,-y+1,-z1
crystal symmetry operation2_665x+1,-y+1,-z1
crystal symmetry operation2_765x+2,-y+1,-z1
crystal symmetry operation2_865x+3,-y+1,-z1
Unit cell
Length a, b, c (Å)56.780, 90.950, 121.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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


Mass: 29919.477 Da / Num. of mol.: 2 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (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 for bacterial expression; N-terminal hexa-His tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DE3 / References: UniProt: O32504
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: long rectangular prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 4.5 mg/mL in 150 mM KCl, 20 mM Tris, pH 7.5 was mixed in 1:1 volume ratio with Wizard Classic 1 (Rigaku) #46 - a solution of 200 mM Lithium sulfate, 10% (w/v) PEG 8000 and 100 mM ...Details: Protein at 4.5 mg/mL in 150 mM KCl, 20 mM Tris, pH 7.5 was mixed in 1:1 volume ratio with Wizard Classic 1 (Rigaku) #46 - a solution of 200 mM Lithium sulfate, 10% (w/v) PEG 8000 and 100 mM Imidazole/ HCl at pH 8.0. The drop was suspended over a 1.5M Ammonium sulfate dehydrating solution and incubated for about 5 weeks.
Temp details: Temperature-controlled incubation

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen gas cryo-stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.747→90.95 Å / Num. obs: 16992 / % possible obs: 99.7 % / Redundancy: 7.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.103 / Rrim(I) all: 0.217 / Χ2: 7.8 / Net I/σ(I): 7.3
Reflection shellResolution: 2.75→2.88 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2181 / CC1/2: 0.355 / Χ2: 0.93 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLM7.2.2data reduction
Aimless0.7.1data scaling
PHASER1.13-2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BDU

6bdu


Resolution: 2.747→51.41 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.93
RfactorNum. reflection% reflection
Rfree0.26 829 4.89 %
Rwork0.2112 --
obs0.2136 16936 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.747→51.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 0 44 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054131
X-RAY DIFFRACTIONf_angle_d0.6575591
X-RAY DIFFRACTIONf_dihedral_angle_d23.6331475
X-RAY DIFFRACTIONf_chiral_restr0.038618
X-RAY DIFFRACTIONf_plane_restr0.004742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7471-2.91920.3811210.33062622X-RAY DIFFRACTION99
2.9192-3.14460.32681550.29142628X-RAY DIFFRACTION100
3.1446-3.4610.27851470.24522639X-RAY DIFFRACTION100
3.461-3.96160.25211340.18972675X-RAY DIFFRACTION100
3.9616-4.99060.23771230.17442713X-RAY DIFFRACTION100
4.9906-51.41940.22821490.19272830X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.5819 Å / Origin y: 37.0496 Å / Origin z: -11.2146 Å
111213212223313233
T0.2551 Å2-0.0388 Å20.0747 Å2-0.2392 Å2-0.0404 Å2--0.2143 Å2
L0.9017 °20.5443 °2-0.4526 °2-0.4944 °2-0.3765 °2--0.2727 °2
S-0.2188 Å °0.0865 Å °-0.1617 Å °-0.1265 Å °0.0954 Å °-0.0872 Å °0.1239 Å °-0.0122 Å °-0.0114 Å °
Refinement TLS groupSelection details: all

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