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- PDB-8sln: Crystal structure of Deinococcus geothermalis PprI complexed with... -

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Basic information

Entry
Database: PDB / ID: 8sln
TitleCrystal structure of Deinococcus geothermalis PprI complexed with ssDNA
Components
  • DNA (29-MER)
  • Zn dependent hydrolase fused to HTH domain, IrrE ortholog
KeywordsHYDROLASE/DNA / DNA damage response / single-stranded DNA / dimer / protease / HYDROLASE / HYDROLASE-DNA complex
Function / homologyIrrE, HTH domain / IrrE N-terminal-like domain / IrrE N-terminal-like domain / hydrolase activity / : / DNA / DNA (> 10) / Zn dependent hydrolase fused to HTH domain, IrrE ortholog
Function and homology information
Biological speciesDeinococcus geothermalis DSM 11300 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhao, Y. / Lu, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870051 China
CitationJournal: Nat Commun / Year: 2024
Title: The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA.
Authors: Lu, H. / Chen, Z. / Xie, T. / Zhong, S. / Suo, S. / Song, S. / Wang, L. / Xu, H. / Tian, B. / Zhao, Y. / Zhou, R. / Hua, Y.
History
DepositionApr 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zn dependent hydrolase fused to HTH domain, IrrE ortholog
D: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4603
Polymers40,4052
Non-polymers551
Water00
1
A: Zn dependent hydrolase fused to HTH domain, IrrE ortholog
D: DNA (29-MER)
hetero molecules

A: Zn dependent hydrolase fused to HTH domain, IrrE ortholog
D: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9216
Polymers80,8114
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6830 Å2
ΔGint-45 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.990, 84.990, 88.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Zn dependent hydrolase fused to HTH domain, IrrE ortholog


Mass: 31556.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis DSM 11300 (bacteria)
Gene: Dgeo_0395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1J1D6
#2: DNA chain DNA (29-MER)


Mass: 8848.692 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.3 M potassium sodium tartrate tetrahydrate, 20% polyethylene glycol 3350, and 2.5 mM MnCl2

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 19166 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.038 / Net I/σ(I): 22.23
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.260.48413960.9440.5351
2.26-2.320.31613750.9780.3491
2.32-2.390.27313130.9820.3011
2.39-2.460.22312830.9910.2451
2.46-2.540.17112490.9940.1881
2.54-2.630.12412060.9970.1361
2.63-2.730.09311860.9970.1021
2.73-2.840.08411290.9980.0921
2.84-2.970.06410710.9990.071
2.97-3.110.05210390.9990.0571
3.11-3.280.04210050.9990.0461
3.28-3.480.0359200.9990.0381
3.48-3.720.0391010.0331
3.72-4.020.0298130.9990.0321
4.02-4.40.0287650.9990.0311
4.4-4.920.02670810.0281
4.92-5.680.0266120.9990.0291
5.68-6.960.0275270.9990.031
6.96-9.840.0244210.9990.0271
9.84-300.0232380.9990.0261

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.54 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 927 4.87 %
Rwork0.2371 --
obs0.2385 19049 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 224 1 0 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082106
X-RAY DIFFRACTIONf_angle_d0.962903
X-RAY DIFFRACTIONf_dihedral_angle_d24.162798
X-RAY DIFFRACTIONf_chiral_restr0.073338
X-RAY DIFFRACTIONf_plane_restr0.009342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.40971420.34712519X-RAY DIFFRACTION99
2.32-2.460.34611330.30512532X-RAY DIFFRACTION99
2.46-2.650.34861400.32122540X-RAY DIFFRACTION99
2.65-2.920.34461280.33952577X-RAY DIFFRACTION100
2.92-3.340.29471300.29652600X-RAY DIFFRACTION100
3.34-4.20.26571210.23312631X-RAY DIFFRACTION100
4.2-26.540.21631330.18192723X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.2261 Å / Origin y: -33.8314 Å / Origin z: -8.1595 Å
111213212223313233
T0.3959 Å20.0356 Å2-0.0494 Å2-0.6283 Å2-0.0579 Å2--0.447 Å2
L2.3313 °21.1981 °2-3.0073 °2-1.5954 °2-2.2486 °2--7.2541 °2
S0.1385 Å °-0.4195 Å °0.1891 Å °0.3458 Å °-0.0286 Å °-0.1019 Å °-0.4945 Å °0.443 Å °-0.0853 Å °
Refinement TLS groupSelection details: not water

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