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

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Basic information

Entry
Database: PDB / ID: 8qjn
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia in complex with adenosine-5'-monophosphate
ComponentsS1/P1 Nuclease
KeywordsHYDROLASE / Nuclease
Function / homologyADENOSINE MONOPHOSPHATE / PHOSPHATE ION / :
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)57,92514
Polymers56,7102
Non-polymers1,21512
Water10,611589
1
A: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7436
Polymers28,3551
Non-polymers3885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1818
Polymers28,3551
Non-polymers8277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.470, 72.741, 82.752
Angle α, β, γ (deg.)90.000, 102.684, 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, 601 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium sulfate 0.1 M MES pH 6.5, 30% w/v Polyethylene glycol 8000. Protein concentration 8.5 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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→43.385 Å / Num. obs: 52701 / % possible obs: 88.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.113 / Net I/σ(I): 13.2
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2636 / CC1/2: 0.777 / Rrim(I) all: 0.935 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.385 Å / Cor.coef. Fo:Fc: 0.956 / SU B: 2.184 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.111
Details: Hydrogens have been added in their riding positions. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2536 5 %Random
Rwork0.1747 52701 --
all0.176 ---
obs0.1759 52701 85.069 %-
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: 19.032 Å2
Baniso -1Baniso -2Baniso -3
1-0.156 Å20 Å20.37 Å2
2---0.33 Å2-0 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 55 589 4453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134045
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153786
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.6445512
X-RAY DIFFRACTIONr_angle_other_deg1.4691.598677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66420.938256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05515668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3531546
X-RAY DIFFRACTIONr_chiral_restr0.0860.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
X-RAY DIFFRACTIONr_nbd_refined0.2230.2993
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23622
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21961
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2425
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1440.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.217
X-RAY DIFFRACTIONr_nbd_other0.1840.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.231
X-RAY DIFFRACTIONr_mcbond_it1.6311.7191984
X-RAY DIFFRACTIONr_mcbond_other1.6221.7161982
X-RAY DIFFRACTIONr_mcangle_it2.5612.5742484
X-RAY DIFFRACTIONr_mcangle_other2.5552.5732484
X-RAY DIFFRACTIONr_scbond_it2.5352.0612061
X-RAY DIFFRACTIONr_scbond_other2.4612.042049
X-RAY DIFFRACTIONr_scangle_it3.8952.973013
X-RAY DIFFRACTIONr_scangle_other3.8622.942996
X-RAY DIFFRACTIONr_lrange_it6.14322.0454974
X-RAY DIFFRACTIONr_lrange_other5.81621.1524795
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69300.2473105X-RAY DIFFRACTION68.2568
1.693-1.73900.2623179X-RAY DIFFRACTION71.7122
1.739-1.78900.2373255X-RAY DIFFRACTION75.3996
1.789-1.84400.2183322X-RAY DIFFRACTION78.6645
1.844-1.90500.2513480X-RAY DIFFRACTION85.82
1.905-1.97200.2643081X-RAY DIFFRACTION78.198
1.972-2.04600.1973610X-RAY DIFFRACTION95.4521
2.046-2.1300.2052995X-RAY DIFFRACTION80.9022
2.13-2.22400.183217X-RAY DIFFRACTION92.1249
2.224-2.33300.1722950X-RAY DIFFRACTION87.5891
2.333-2.45900.1423041X-RAY DIFFRACTION95.3292
2.459-2.60800.1372930X-RAY DIFFRACTION96.3816
2.608-2.78800.1412493X-RAY DIFFRACTION87.1983
2.788-3.01100.1352508X-RAY DIFFRACTION95.1803
3.011-3.29700.1442388X-RAY DIFFRACTION96.9943
3.297-3.68600.1511867X-RAY DIFFRACTION84.0612
3.686-4.25500.1281710X-RAY DIFFRACTION87.7373
4.255-5.20700.1511620X-RAY DIFFRACTION97.2389
5.207-7.34900.2381254X-RAY DIFFRACTION96.3134
7.349-43.38500.21697X-RAY DIFFRACTION94.4444

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