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- PDB-8qjp: SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with... -

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Basic information

Entry
Database: PDB / ID: 8qjp
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia in complex with uridine - 5'- monophosphate
ComponentsS1/P1 Nuclease
KeywordsHYDROLASE / Nuclease
Function / homologyPHOSPHATE ION / URIDINE-5'-MONOPHOSPHATE / :
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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

Downloads & links

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Assembly

Deposited unit
A: S1/P1 Nuclease
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,68620
Polymers56,7102
Non-polymers1,97718
Water12,989721
1
A: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,33610
Polymers28,3551
Non-polymers9819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,35010
Polymers28,3551
Non-polymers9969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.434, 72.800, 82.928
Angle α, β, γ (deg.)90.000, 102.302, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein S1/P1 Nuclease


Mass: 28354.814 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 739 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 30 % w/v PEG 8000, 0.2 M Lithium sulfate. Protein concentration 11.8 mg/ml. Cryo-protection by glycerol 20 % v/v.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.2→43.41 Å / Num. obs: 155893 / % possible obs: 97 % / Redundancy: 5.1 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7417 / CC1/2: 0.579 / Rrim(I) all: 1.352 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→43.41 Å / Cor.coef. Fo:Fc: 0.979 / SU B: 1.351 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.034
Details: Hydrogens have been added in their riding positions. Data were corrected for lattice translocation defect by applying approach as in doi: 10.1107/S2059798322008397. Last refinement cycle was ...Details: Hydrogens have been added in their riding positions. Data were corrected for lattice translocation defect by applying approach as in doi: 10.1107/S2059798322008397. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 7501 5 %random
Rwork0.1339 155884 --
all0.137 ---
obs0.1369 155884 96.934 %-
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: 20.454 Å2
Baniso -1Baniso -2Baniso -3
1-1.358 Å20 Å20.578 Å2
2---1.124 Å20 Å2
3----0.444 Å2
Refinement stepCycle: LAST / Resolution: 1.2→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3857 0 104 721 4682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134142
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153876
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6435638
X-RAY DIFFRACTIONr_angle_other_deg1.5731.5938889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69720.846260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43615678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5581547
X-RAY DIFFRACTIONr_chiral_restr0.0980.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024859
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined0.2280.2977
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.23671
X-RAY DIFFRACTIONr_nbtor_refined0.170.22016
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2461
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.227
X-RAY DIFFRACTIONr_nbd_other0.2480.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0170.21
X-RAY DIFFRACTIONr_mcbond_it1.7851.7552006
X-RAY DIFFRACTIONr_mcbond_other1.7763.982004
X-RAY DIFFRACTIONr_mcangle_it2.1072.652512
X-RAY DIFFRACTIONr_mcangle_other2.0992.8432512
X-RAY DIFFRACTIONr_scbond_it2.8352.1572136
X-RAY DIFFRACTIONr_scbond_other2.8229999.9992121
X-RAY DIFFRACTIONr_scangle_it3.2673.1083110
X-RAY DIFFRACTIONr_scangle_other3.2743.0953093
X-RAY DIFFRACTIONr_lrange_it3.829999.2355072
X-RAY DIFFRACTIONr_lrange_other3.4429999.0474859
X-RAY DIFFRACTIONr_rigid_bond_restr3.10534128
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.23100.27211185X-RAY DIFFRACTION94.428
1.231-1.26500.25211057X-RAY DIFFRACTION95.9976
1.265-1.30200.23410841X-RAY DIFFRACTION96.2361
1.302-1.34200.21210544X-RAY DIFFRACTION96.6896
1.342-1.38600.19810074X-RAY DIFFRACTION95.1904
1.386-1.43400.1729914X-RAY DIFFRACTION96.5712
1.434-1.48800.1469560X-RAY DIFFRACTION97.0066
1.488-1.54900.1229263X-RAY DIFFRACTION97.0456
1.549-1.61800.1118926X-RAY DIFFRACTION98.0556
1.618-1.69700.0988518X-RAY DIFFRACTION97.6163
1.697-1.78900.0927981X-RAY DIFFRACTION96.0872
1.789-1.89700.0897761X-RAY DIFFRACTION98.4773
1.897-2.02800.0977300X-RAY DIFFRACTION98.622
2.028-2.1900.1036785X-RAY DIFFRACTION98.9644
2.19-2.39900.1026180X-RAY DIFFRACTION97.6458
2.399-2.68200.115615X-RAY DIFFRACTION97.4488
2.682-3.09600.1275032X-RAY DIFFRACTION99.1136
3.096-3.79100.1344251X-RAY DIFFRACTION98.38
3.791-5.35500.153219X-RAY DIFFRACTION96.5217
5.355-43.4100.231878X-RAY DIFFRACTION99.26

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