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- PDB-8qjl: SmNuc1 nuclease from Stenotrophomonas maltophilia -

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Basic information

Entry
Database: PDB / ID: 8qjl
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia
ComponentsS1/P1 Nuclease
KeywordsHYDROLASE / Nuclease
Function / homology:
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAdamkova, K. / Koval, T. / Kolenko, P. / Dohnalek, J.
Funding support Czech Republic, European Union, 4items
OrganizationGrant numberCountry
Czech Science Foundation23-06295S Czech Republic
Czech Academy of Sciences86652036 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/18_046/0015974European Union
CitationJournal: Febs J. / Year: 2025
Title: Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study.
Authors: Adamkova, K. / Trundova, M. / Koval, T. / Hustakova, B. / Kolenko, P. / Duskova, J. / Skalova, T. / Dohnalek, J.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0239
Polymers28,3551
Non-polymers6698
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.470, 72.970, 49.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-562-

HOH

21A-721-

HOH

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Components

#1: Protein S1/P1 Nuclease


Mass: 28354.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence type 5, study in PMID: 28894437
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: SanG_2012 / Gene: A1OC_03585 / Plasmid: pET303/CT-His_SmNuc1 / Details (production host): MalE signal peptide / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J7SYS2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.9 % / Description: Long rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350. Protein concentration 7.5 mg/ml. Cryo-protection by glycerol 20 % v/v.
Temp details: Controlled

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Oct 14, 2019 / Details: HELIOS MX, Ga
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.4→41.22 Å / Num. obs: 50815 / % possible obs: 96 % / Redundancy: 14.3 % / Biso Wilson estimate: 8.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.122 / Net I/σ(I): 19.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.166 / Num. unique obs: 2541 / CC1/2: 0.509 / Rrim(I) all: 1.32 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.22 Å / Cor.coef. Fo:Fc: 0.978 / SU B: 1.202 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.051
Details: Hydrogens have been added in their riding positions. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.1612 2516 5 %Random
Rwork0.1186 50768 --
all0.123 ---
obs0.1228 50768 95.923 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.934 Å2
Baniso -1Baniso -2Baniso -3
1-0.242 Å20 Å20 Å2
2---0.052 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 30 455 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132139
X-RAY DIFFRACTIONr_bond_other_d0.0070.0152020
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6462935
X-RAY DIFFRACTIONr_angle_other_deg1.6121.5964644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21920.78141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90715363
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg13.792152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0131526
X-RAY DIFFRACTIONr_chiral_restr0.1150.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined0.2250.2518
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.21918
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21017
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2304
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.213
X-RAY DIFFRACTIONr_nbd_other0.1950.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.460.21
X-RAY DIFFRACTIONr_mcbond_it1.2281.0931030
X-RAY DIFFRACTIONr_mcbond_other1.191.091029
X-RAY DIFFRACTIONr_mcangle_it1.4861.6561299
X-RAY DIFFRACTIONr_mcangle_other1.4861.6591300
X-RAY DIFFRACTIONr_scbond_it2.0221.4171108
X-RAY DIFFRACTIONr_scbond_other2.0211.4181109
X-RAY DIFFRACTIONr_scangle_it2.2942.0151612
X-RAY DIFFRACTIONr_scangle_other2.2942.0171613
X-RAY DIFFRACTIONr_lrange_it3.6699992728
X-RAY DIFFRACTIONr_lrange_other2.1768599.8072561
X-RAY DIFFRACTIONr_rigid_bond_restr1.90134137
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43600.2423791X-RAY DIFFRACTION98.4675
1.436-1.47600.1713774X-RAY DIFFRACTION99.9206
1.476-1.51800.193050X-RAY DIFFRACTION83.3561
1.518-1.56500.1453019X-RAY DIFFRACTION85.0423
1.565-1.61600.1153463X-RAY DIFFRACTION100
1.616-1.67300.0973330X-RAY DIFFRACTION100
1.673-1.73600.0853243X-RAY DIFFRACTION100
1.736-1.80700.0853096X-RAY DIFFRACTION100
1.807-1.88700.0862988X-RAY DIFFRACTION100
1.887-1.97900.12865X-RAY DIFFRACTION100
1.979-2.08600.0992741X-RAY DIFFRACTION100
2.086-2.21200.0962584X-RAY DIFFRACTION99.9613
2.212-2.36500.0982055X-RAY DIFFRACTION84.4289
2.365-2.55400.1071987X-RAY DIFFRACTION87.3407
2.554-2.79700.1041941X-RAY DIFFRACTION91.4272
2.797-3.12600.1191918X-RAY DIFFRACTION100
3.126-3.60700.1331610X-RAY DIFFRACTION94.7616
3.607-4.41200.121466X-RAY DIFFRACTION100
4.412-6.21700.1751157X-RAY DIFFRACTION100
6.217-41.2200.22690X-RAY DIFFRACTION99.1379

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