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- PDB-8slm: Crystal structure of Deinococcus geothermalis PprI -

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Basic information

Entry
Database: PDB / ID: 8slm
TitleCrystal structure of Deinococcus geothermalis PprI
ComponentsZn dependent hydrolase fused to HTH domain, IrrE ortholog
KeywordsHYDROLASE / DNA damage response / metal ion binding / dimer / protease
Function / homologyIrrE, HTH domain / : / IrrE N-terminal-like domain / IrrE N-terminal-like domain / hydrolase activity / metal ion binding / : / Zn dependent hydrolase fused to HTH domain, IrrE ortholog
Function and homology information
Biological speciesDeinococcus geothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7083
Polymers31,5571
Non-polymers1512
Water00
1
A: Zn dependent hydrolase fused to HTH domain, IrrE ortholog
hetero molecules

A: Zn dependent hydrolase fused to HTH domain, IrrE ortholog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4156
Polymers63,1132
Non-polymers3024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area1720 Å2
ΔGint-57 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.770, 120.770, 100.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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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 (bacteria) / Strain: DSM 11300 / Gene: Dgeo_0395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1J1D6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.7 M (NH4)2SO4, 0.1 M Bis-tris (pH 6.5), 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: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 10704 / % possible obs: 96.9 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.047 / Net I/σ(I): 21.44
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.81-2.880.5417830.820.6211
2.88-2.960.3757760.8950.4291
2.96-3.050.2997450.920.3421
3.05-3.140.2097270.9630.2381
3.14-3.240.1576920.9790.1791
3.24-3.360.1056980.9920.121
3.36-3.480.0796520.9950.091
3.48-3.630.0676330.9960.0761
3.63-3.790.0536110.9970.061
3.79-3.970.0435800.9980.0491
3.97-4.190.0335590.9990.0381
4.19-4.440.0315270.9980.0361
4.44-4.750.0284890.9990.0321
4.75-5.130.034550.9980.0341
5.13-5.620.034270.9990.0351
5.62-6.280.0313870.9990.0351
6.28-7.250.0253350.9990.0281
7.25-8.880.0212870.9990.0241
8.88-12.560.0192230.9990.0221
12.56-300.0231180.9980.0271

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→29.33 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 526 4.91 %
Rwork0.247 --
obs0.2489 10704 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 6 0 1840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121874
X-RAY DIFFRACTIONf_angle_d1.4012549
X-RAY DIFFRACTIONf_dihedral_angle_d13.965687
X-RAY DIFFRACTIONf_chiral_restr0.096301
X-RAY DIFFRACTIONf_plane_restr0.002333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-3.090.29621270.30942534X-RAY DIFFRACTION99
3.09-3.540.33071280.28662536X-RAY DIFFRACTION99
3.54-4.460.31621360.23982543X-RAY DIFFRACTION98
4.46-29.330.24841350.22782565X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 35.9638 Å / Origin y: 31.784 Å / Origin z: 7.5873 Å
111213212223313233
T0.4693 Å20.0436 Å2-0.1652 Å2-0.4397 Å20.0194 Å2--0.5302 Å2
L5.9673 °2-1.8771 °2-2.0394 °2-2.7423 °20.4872 °2--4.1488 °2
S-0.2218 Å °-0.2972 Å °-0.4414 Å °0.5002 Å °0.3186 Å °-0.0563 Å °0.3745 Å °-0.1069 Å °-0.0609 Å °
Refinement TLS groupSelection details: all

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