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- PDB-6bdu: Crystal structure of PprA from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 6bdu
TitleCrystal structure of PprA from Deinococcus radiodurans
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN / DNA damage repair / Radiation induced / Genome segregation / Filment 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 / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSzabla, R. / Czerwinski, M. / Junop, M.S.
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
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 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 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)67,2062
Polymers67,2062
Non-polymers00
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer interface was observed in crystal structure of PprA from D.radiodurans, D.peraridilitoris and D.deserti.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-8 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.629, 99.149, 116.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 33602.750 Da / Num. of mol.: 2 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (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 / Cell line (production host): B834(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: O32504
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.53 % / Description: square prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 2.4mg/mL in 150mM KCl, 20mM Tris, pH 7.5 was mixed in 1:1 volume ratio with a solution of 0.2 M Lithium Citrate Tribasic and 20 % (w/v) PEG 3350. The drop was suspended over 1.5M Ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→58.34 Å / Num. obs: 45262 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.061 / Rrim(I) all: 0.159 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3281 / CC1/2: 0.658 / Rpim(I) all: 0.662 / Rrim(I) all: 1.606

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.21 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34
RfactorNum. reflection% reflection
Rfree0.2357 2315 5.12 %
Rwork0.205 --
obs0.2065 45188 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→36.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 0 376 4446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054140
X-RAY DIFFRACTIONf_angle_d0.6885600
X-RAY DIFFRACTIONf_dihedral_angle_d20.6171488
X-RAY DIFFRACTIONf_chiral_restr0.048616
X-RAY DIFFRACTIONf_plane_restr0.004744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04090.32741350.30382510X-RAY DIFFRACTION100
2.0409-2.08520.32941310.27852456X-RAY DIFFRACTION100
2.0852-2.13370.3291140.26392501X-RAY DIFFRACTION100
2.1337-2.18710.32091510.24212492X-RAY DIFFRACTION100
2.1871-2.24620.31071230.24012498X-RAY DIFFRACTION100
2.2462-2.31230.29881240.24222481X-RAY DIFFRACTION100
2.3123-2.38690.28311420.23032485X-RAY DIFFRACTION100
2.3869-2.47220.25721420.23492511X-RAY DIFFRACTION100
2.4722-2.57120.28271400.22632489X-RAY DIFFRACTION100
2.5712-2.68810.29651330.24162512X-RAY DIFFRACTION100
2.6881-2.82980.27211630.23122495X-RAY DIFFRACTION100
2.8298-3.0070.27621390.21692513X-RAY DIFFRACTION100
3.007-3.23910.2881360.21082504X-RAY DIFFRACTION100
3.2391-3.56480.20691500.19912546X-RAY DIFFRACTION100
3.5648-4.080.18251190.17592574X-RAY DIFFRACTION100
4.08-5.1380.17381190.162605X-RAY DIFFRACTION100
5.138-36.21590.17651540.17982701X-RAY DIFFRACTION100

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