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- PDB-6a28: Crystal structure of PprA W183R mutant form 2 -

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Basic information

Entry
Database: PDB / ID: 6a28
TitleCrystal structure of PprA W183R mutant form 2
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN
Function / homologycellular response to desiccation / positive regulation of DNA ligation / cellular response to gamma radiation / 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 / FOURIER SYNTHESIS / Resolution: 2.193 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)61,6633
Polymers61,5672
Non-polymers961
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-12 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.226, 79.293, 264.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 30783.566 Da / Num. of mol.: 2 / Mutation: W183R
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32504
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
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: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97965 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.193→46.9 Å / Num. obs: 30255 / % possible obs: 94.8 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 36.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1496 / % possible all: 92.3

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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: 6A29

6a29


Resolution: 2.193→32.108 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1510 5 %Random selection
Rwork0.1898 ---
obs0.1921 30195 94.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.193→32.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 5 232 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083584
X-RAY DIFFRACTIONf_angle_d1.0854867
X-RAY DIFFRACTIONf_dihedral_angle_d16.0911265
X-RAY DIFFRACTIONf_chiral_restr0.043546
X-RAY DIFFRACTIONf_plane_restr0.004649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1929-2.26370.26591300.2082456X-RAY DIFFRACTION90
2.2637-2.34460.26611350.19442583X-RAY DIFFRACTION94
2.3446-2.43840.25551330.19472533X-RAY DIFFRACTION94
2.4384-2.54930.25171340.19972540X-RAY DIFFRACTION94
2.5493-2.68370.22191340.19542545X-RAY DIFFRACTION93
2.6837-2.85170.25791350.21412573X-RAY DIFFRACTION94
2.8517-3.07170.29051360.20712581X-RAY DIFFRACTION93
3.0717-3.38050.271350.20432541X-RAY DIFFRACTION94
3.3805-3.8690.22981390.18132662X-RAY DIFFRACTION96
3.869-4.87180.18411480.16332789X-RAY DIFFRACTION99
4.8718-32.1110.23141510.19342882X-RAY DIFFRACTION99

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