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- PDB-6a27: Crystal structure of PprA W183R mutant form 1 -

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Basic information

Entry
Database: PDB / ID: 6a27
TitleCrystal structure of PprA W183R mutant form 1
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN
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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.353 Å
AuthorsAdachi, M. / Shibazaki, C. / Shimizu, R. / Arai, S. / Satoh, K. / Narumi, I. / Kuroki, R.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19370046 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19380054 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16KT0063 Japan
CitationJournal: FASEB J. / Year: 2019
Title: Extended structure of pleiotropic DNA repair-promoting protein PprA from Deinococcus radiodurans.
Authors: Adachi, M. / Shimizu, R. / Shibazaki, C. / Satoh, K. / Fujiwara, S. / Arai, S. / Narumi, I. / Kuroki, R.
History
DepositionJun 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: DNA repair protein PprA
B: DNA repair protein PprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2864
Polymers61,0982
Non-polymers1882
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-20 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.459, 99.357, 48.101
Angle α, β, γ (deg.)90.00, 110.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30549.098 Da / Num. of mol.: 2 / Mutation: W183R
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32504
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 1.6 Å3/Da / Density % sol: 22.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris buffer (pH 8.5) containing 0.2 M LiSO4 and 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→25.72 Å / Num. obs: 76916 / % possible obs: 92.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 33.8
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7671 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6A28

6a28


Resolution: 1.353→25.72 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 3845 5 %RANDOM
Rwork0.1778 ---
obs0.179 76889 92.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.353→25.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 11 500 3560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053116
X-RAY DIFFRACTIONf_angle_d1.0344226
X-RAY DIFFRACTIONf_dihedral_angle_d14.1631098
X-RAY DIFFRACTIONf_chiral_restr0.064461
X-RAY DIFFRACTIONf_plane_restr0.005563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3529-1.370.32261320.26092508X-RAY DIFFRACTION86
1.37-1.3880.27171440.25712733X-RAY DIFFRACTION94
1.388-1.4070.27541440.24142748X-RAY DIFFRACTION94
1.407-1.42710.24741460.22962767X-RAY DIFFRACTION95
1.4271-1.44840.25771480.2222806X-RAY DIFFRACTION94
1.4484-1.47110.23691450.21942773X-RAY DIFFRACTION96
1.4711-1.49520.24731480.19992786X-RAY DIFFRACTION94
1.4952-1.5210.24261440.20332743X-RAY DIFFRACTION95
1.521-1.54860.23181470.19122798X-RAY DIFFRACTION94
1.5486-1.57840.23381440.1882719X-RAY DIFFRACTION95
1.5784-1.61060.20251450.18182757X-RAY DIFFRACTION93
1.6106-1.64560.23231450.1742779X-RAY DIFFRACTION95
1.6456-1.68390.18231440.16992721X-RAY DIFFRACTION93
1.6839-1.7260.21011440.17062745X-RAY DIFFRACTION94
1.726-1.77270.18371450.17532735X-RAY DIFFRACTION93
1.7727-1.82480.22291410.16932676X-RAY DIFFRACTION92
1.8248-1.88370.19611420.16932717X-RAY DIFFRACTION91
1.8837-1.9510.18971400.16762663X-RAY DIFFRACTION92
1.951-2.02910.17831410.16632667X-RAY DIFFRACTION91
2.0291-2.12140.2021400.16622661X-RAY DIFFRACTION91
2.1214-2.23320.19451390.15972628X-RAY DIFFRACTION90
2.2332-2.3730.1911390.16452657X-RAY DIFFRACTION90
2.373-2.55610.18231390.1682659X-RAY DIFFRACTION90
2.5561-2.8130.2271440.18522725X-RAY DIFFRACTION93
2.813-3.21940.18451500.1672855X-RAY DIFFRACTION97
3.2194-4.05350.16511460.1612766X-RAY DIFFRACTION94
4.0535-25.72470.22451190.20492252X-RAY DIFFRACTION75

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