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- PDB-6a29: Crystal structure of PprA A139R mutant -

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Basic information

Entry
Database: PDB / ID: 6a29
TitleCrystal structure of PprA A139R mutant
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: 2.399 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 1.2Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein PprA
B: DNA repair protein PprA
C: DNA repair protein PprA
D: DNA repair protein PprA
E: DNA repair protein PprA
F: DNA repair protein PprA
G: DNA repair protein PprA
H: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)245,3148
Polymers245,3148
Non-polymers00
Water9,278515
1
A: DNA repair protein PprA
B: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)61,3282
Polymers61,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-14 kcal/mol
Surface area26570 Å2
MethodPISA
2
C: DNA repair protein PprA
D: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)61,3282
Polymers61,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-11 kcal/mol
Surface area27300 Å2
MethodPISA
3
E: DNA repair protein PprA
F: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)61,3282
Polymers61,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-12 kcal/mol
Surface area27620 Å2
MethodPISA
4
G: DNA repair protein PprA
H: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)61,3282
Polymers61,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.190, 272.260, 104.887
Angle α, β, γ (deg.)90.00, 98.64, 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: 30664.227 Da / Num. of mol.: 8 / Mutation: A139R
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
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% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.399→48.631 Å / Num. obs: 106269 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 31.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5354 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.399→48.631 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 5258 5 %RANDOM
Rwork0.2124 ---
obs0.2154 105142 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.399→48.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16690 0 0 515 17205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916970
X-RAY DIFFRACTIONf_angle_d1.1622978
X-RAY DIFFRACTIONf_dihedral_angle_d17.4626100
X-RAY DIFFRACTIONf_chiral_restr0.0462531
X-RAY DIFFRACTIONf_plane_restr0.0043077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3987-2.42590.34551930.28313142X-RAY DIFFRACTION94
2.4259-2.45450.35921580.27443396X-RAY DIFFRACTION100
2.4545-2.48440.32841750.2793289X-RAY DIFFRACTION100
2.4844-2.51580.36591780.25783313X-RAY DIFFRACTION100
2.5158-2.54890.31091670.25053398X-RAY DIFFRACTION100
2.5489-2.58390.29591660.24593421X-RAY DIFFRACTION100
2.5839-2.62080.36221790.24043288X-RAY DIFFRACTION100
2.6208-2.65990.35011860.2413332X-RAY DIFFRACTION100
2.6599-2.70140.31811940.23863323X-RAY DIFFRACTION100
2.7014-2.74570.28811750.22063386X-RAY DIFFRACTION100
2.7457-2.79310.27041670.22443330X-RAY DIFFRACTION100
2.7931-2.84390.30691720.21563374X-RAY DIFFRACTION100
2.8439-2.89850.29441840.23133373X-RAY DIFFRACTION100
2.8985-2.95770.3141710.23573305X-RAY DIFFRACTION100
2.9577-3.0220.35921700.23363370X-RAY DIFFRACTION100
3.022-3.09230.29381880.23633388X-RAY DIFFRACTION100
3.0923-3.16960.27721700.23053306X-RAY DIFFRACTION100
3.1696-3.25530.30191940.21693379X-RAY DIFFRACTION100
3.2553-3.35110.29991600.2173331X-RAY DIFFRACTION100
3.3511-3.45920.29131760.22583357X-RAY DIFFRACTION100
3.4592-3.58280.27681760.21333383X-RAY DIFFRACTION100
3.5828-3.72620.28911780.20683374X-RAY DIFFRACTION100
3.7262-3.89570.27371720.20133339X-RAY DIFFRACTION100
3.8957-4.1010.2391750.20113395X-RAY DIFFRACTION100
4.101-4.35780.24831800.18983313X-RAY DIFFRACTION100
4.3578-4.6940.22941700.18293346X-RAY DIFFRACTION100
4.694-5.16590.25011870.19933336X-RAY DIFFRACTION100
5.1659-5.91230.2611720.21813382X-RAY DIFFRACTION100
5.9123-7.44460.21481760.19383370X-RAY DIFFRACTION100
7.4446-48.64110.23291490.19822845X-RAY DIFFRACTION83

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