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- PDB-6mc8: Crystal structure of PprA dimer from Deinococcus deserti -

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Basic information

Entry
Database: PDB / ID: 6mc8
TitleCrystal structure of PprA dimer from Deinococcus deserti
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN / DNA damage repair / Radiation induced / Genome segregation / Filament formation
Function / homologyAspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / aspartic-type endopeptidase activity / proteolysis / Putative DNA repair protein PprA
Function and homology information
Biological speciesDeinococcus deserti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 from Deinococcus radiodurans
Authors: Szabla, R. / Czerwinski, M. / Junop, M.S.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)67,2642
Polymers67,2642
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, This dimer interface is present in all crystal structures of PprA, despite differences in Deinococcus species of origin and crystal packing. PprA from D. radiodurans harboring ...Evidence: homology, This dimer interface is present in all crystal structures of PprA, despite differences in Deinococcus species of origin and crystal packing. PprA from D. radiodurans harboring this analogous mutation exists exclusively as a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-3 kcal/mol
Surface area26940 Å2
Unit cell
Length a, b, c (Å)54.417, 80.985, 148.868
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


Mass: 33631.777 Da / Num. of mol.: 2 / Mutation: D192K, D196K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus deserti (strain VCD115 / DSM 17065 / LMG 22923) (bacteria)
Strain: VCD115 / DSM 17065 / LMG 22923 / Gene: pprA, Deide_2p01380 / Plasmid: pDEST-527
Details (production host): Gateway destination vector for bacterial expression; His tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C1D318
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.59 Å3/Da / Density % sol: 52.51 % / Description: square bipyramid
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Protein at 3.0 mg/mL in 800 mM NaCl, 150 mM Imidazole, 20 mM Tris, pH 8.0 was mixed in 1:1 volume ratio with MCSG3 #92 - a solution of 30 % (w/v) PEG 400 and 0.1 M CHES, pH 9.5. The drop was ...Details: Protein at 3.0 mg/mL in 800 mM NaCl, 150 mM Imidazole, 20 mM Tris, pH 8.0 was mixed in 1:1 volume ratio with MCSG3 #92 - a solution of 30 % (w/v) PEG 400 and 0.1 M CHES, pH 9.5. The drop was suspended over 1.5M Ammonium sulfate.
Temp details: Constant-temperature incubation

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen gas cryostream
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.5→28.72 Å / Num. obs: 22737 / % possible obs: 96.7 % / Redundancy: 24.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.049 / Rrim(I) all: 0.189 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2 / Num. unique obs: 2079 / CC1/2: 0.845 / Rpim(I) all: 0.223 / Rrim(I) all: 0.7 / % possible all: 80.2

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
CrysalisPro39.29cdata reduction
StructureStudio2.4data collection
PHASER1.13-2998phasing
Aimless0.5.32data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.72 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.261 1131 5 %
Rwork0.2466 --
obs-22571 96.16 %
Refinement stepCycle: LAST / Resolution: 2.5→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 0 174 4309

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