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

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Basic information

Entry
Database: PDB / ID: 8qjq
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine - 5' - monophosphate as an inhibitor.
ComponentsS1/P1 Nuclease
KeywordsHYDROLASE / Nuclease
Function / homologyCYTIDINE-5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / :
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)60,29335
Polymers56,7102
Non-polymers3,58433
Water7,530418
1
A: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,22119
Polymers28,3551
Non-polymers1,86618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,07216
Polymers28,3551
Non-polymers1,71715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.255, 73.166, 81.660
Angle α, β, γ (deg.)90.000, 104.991, 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 , 8 types, 451 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-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 25 % w/v PEG 3350, 0.2 M Lithium sulfate, cryo-protection 25% v/v glycerol, protein concentration 7.5 mg/ml.
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: 1.8→41.78 Å / Num. obs: 45358 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.117 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2614 / CC1/2: 0.699 / Rrim(I) all: 1.153 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.78 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 2.464 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.124
Details: Hydrogens have been added in their riding positions. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 2212 5 %Random
Rwork0.1663 45328 --
all0.167 ---
obs0.1675 45328 99.316 %-
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: 29.076 Å2
Baniso -1Baniso -2Baniso -3
1-1.031 Å20 Å2-0.769 Å2
2---1.087 Å2-0 Å2
3---0.409 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 188 418 4496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134207
X-RAY DIFFRACTIONr_bond_other_d0.0040.0153864
X-RAY DIFFRACTIONr_ext_dist_refined_d00.019
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6425727
X-RAY DIFFRACTIONr_angle_other_deg1.3511.5938854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.21820.811259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75415669
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg10.906152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0241547
X-RAY DIFFRACTIONr_chiral_restr0.0710.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined0.2150.2987
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.23570
X-RAY DIFFRACTIONr_nbtor_refined0.1550.21973
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2306
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.251
X-RAY DIFFRACTIONr_nbd_other0.2320.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.227
X-RAY DIFFRACTIONr_mcbond_it2.1142.792015
X-RAY DIFFRACTIONr_mcbond_other2.1132.7872014
X-RAY DIFFRACTIONr_mcangle_it3.2594.1722522
X-RAY DIFFRACTIONr_mcangle_other3.2584.1752523
X-RAY DIFFRACTIONr_scbond_it2.6743.2442192
X-RAY DIFFRACTIONr_scbond_other2.4693.1772109
X-RAY DIFFRACTIONr_scangle_it4.0534.723195
X-RAY DIFFRACTIONr_scangle_other3.9324.6173070
X-RAY DIFFRACTIONr_lrange_it6.47734.114871
X-RAY DIFFRACTIONr_lrange_other6.24133.5374754
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84700.283250X-RAY DIFFRACTION98.6044
1.847-1.89700.2453278X-RAY DIFFRACTION99.1831
1.897-1.95200.2323185X-RAY DIFFRACTION99.7807
1.952-2.01200.2053074X-RAY DIFFRACTION99.9025
2.012-2.07800.1852983X-RAY DIFFRACTION99.3671
2.078-2.15100.1692921X-RAY DIFFRACTION99.5569
2.151-2.23200.1642762X-RAY DIFFRACTION99.103
2.232-2.32300.1542664X-RAY DIFFRACTION98.8497
2.323-2.42700.1342569X-RAY DIFFRACTION98.9599
2.427-2.54500.1292483X-RAY DIFFRACTION99.9597
2.545-2.68200.1272345X-RAY DIFFRACTION99.8297
2.682-2.84500.1462230X-RAY DIFFRACTION99.8209
2.845-3.04100.1462099X-RAY DIFFRACTION99.1966
3.041-3.28400.1511915X-RAY DIFFRACTION99.3257
3.284-3.59700.1481775X-RAY DIFFRACTION98.5017
3.597-4.02100.1411637X-RAY DIFFRACTION99.9389
4.021-4.64100.1361446X-RAY DIFFRACTION99.7241
4.641-5.67900.1891227X-RAY DIFFRACTION99.3522
5.679-8.0100.224935X-RAY DIFFRACTION98.0084
8.01-41.7800.295551X-RAY DIFFRACTION99.6383

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