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

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Basic information

Entry
Database: PDB / ID: 8qjo
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-5'-monophosphate
ComponentsS1/P1 Nuclease
KeywordsHYDROLASE / Nuclease
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / :
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)60,44938
Polymers56,7102
Non-polymers3,73936
Water6,828379
1
A: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,46221
Polymers28,3551
Non-polymers2,10820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,98617
Polymers28,3551
Non-polymers1,63216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.178, 73.068, 81.607
Angle α, β, γ (deg.)90.000, 105.324, 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 , 10 types, 415 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350, 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→41.64 Å / Num. obs: 40335 / % possible obs: 96.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.152 / Net I/σ(I): 7.1
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2553 / CC1/2: 0.376 / Rrim(I) all: 1.523 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→41.64 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 3.621 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.144
Details: Hydrogens have been added in their riding positions. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 2029 5 %Random
Rwork0.1714 40318 --
all0.172 ---
obs0.1723 40318 96.312 %-
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: 27.984 Å2
Baniso -1Baniso -2Baniso -3
1-1.471 Å2-0 Å20.222 Å2
2---1.479 Å2-0 Å2
3----0.098 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 197 379 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134126
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153780
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6415613
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5938657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34621.04250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53215648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8431544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
X-RAY DIFFRACTIONr_nbd_refined0.2150.2977
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23584
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21935
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.239
X-RAY DIFFRACTIONr_nbd_other0.2280.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.218
X-RAY DIFFRACTIONr_mcbond_it2.0992.6581980
X-RAY DIFFRACTIONr_mcbond_other2.0992.6571979
X-RAY DIFFRACTIONr_mcangle_it3.2763.9792474
X-RAY DIFFRACTIONr_mcangle_other3.2763.982475
X-RAY DIFFRACTIONr_scbond_it2.8093.112146
X-RAY DIFFRACTIONr_scbond_other2.6863.0512071
X-RAY DIFFRACTIONr_scangle_it4.414.5043134
X-RAY DIFFRACTIONr_scangle_other4.3434.4113021
X-RAY DIFFRACTIONr_lrange_it6.25432.4234737
X-RAY DIFFRACTIONr_lrange_other6.15531.9874652
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89800.3173051X-RAY DIFFRACTION99.155
1.898-1.9500.2952634X-RAY DIFFRACTION88.0053
1.95-2.00600.2712848X-RAY DIFFRACTION98.6491
2.006-2.06800.2542789X-RAY DIFFRACTION96.272
2.068-2.13600.2262452X-RAY DIFFRACTION90.3797
2.136-2.21100.1972667X-RAY DIFFRACTION99.5892
2.211-2.29400.212198X-RAY DIFFRACTION85.692
2.294-2.38800.1712457X-RAY DIFFRACTION99.2727
2.388-2.49400.1612309X-RAY DIFFRACTION97.7561
2.494-2.61500.1422277X-RAY DIFFRACTION99.4323
2.615-2.75700.1352009X-RAY DIFFRACTION93.6597
2.757-2.92400.1322060X-RAY DIFFRACTION99.565
2.924-3.12500.1371900X-RAY DIFFRACTION99.3724
3.125-3.37500.1431745X-RAY DIFFRACTION97.6497
3.375-3.69700.1371650X-RAY DIFFRACTION99.3976
3.697-4.13200.1241487X-RAY DIFFRACTION99.5981
4.132-4.76900.1221301X-RAY DIFFRACTION97.1621
4.769-5.83600.1961114X-RAY DIFFRACTION99.3756
5.836-8.2300.191871X-RAY DIFFRACTION99.5429
8.23-41.6400.19499X-RAY DIFFRACTION97.4609

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