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

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Basic information

Entry
Database: PDB / ID: 8qjm
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine-5'-monophosphate
ComponentsS1/P1 Nuclease
KeywordsHYDROLASE / Nuclease
Function / homologyCYTIDINE-5'-MONOPHOSPHATE / :
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / 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)59,58226
Polymers56,7102
Non-polymers2,87224
Water9,692538
1
A: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,66614
Polymers28,3551
Non-polymers1,31113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1/P1 Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91612
Polymers28,3551
Non-polymers1,56111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.139, 72.805, 81.238
Angle α, β, γ (deg.)90.000, 105.066, 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, 562 molecules

#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 291 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 PEG400 30 % 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 21, 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: 1.65→41.66 Å / Num. obs: 57878 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.961 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.149 / Net I/σ(I): 6.8
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 2787 / CC1/2: 0.559 / Rrim(I) all: 0.722

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→41.66 Å / Cor.coef. Fo:Fc: 0.951 / SU B: 1.689 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.099
Details: Hydrogens have been added in their riding positions. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 2819 5 %Random
Rwork0.1726 57816 --
all0.173 ---
obs0.1732 57816 99.012 %-
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: 12.199 Å2
Baniso -1Baniso -2Baniso -3
1-1.178 Å2-0 Å2-0.898 Å2
2---0.499 Å20 Å2
3----0.171 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 151 538 4569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153884
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.6455717
X-RAY DIFFRACTIONr_angle_other_deg1.4741.5978900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63220.802262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63215677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2961548
X-RAY DIFFRACTIONr_chiral_restr0.0820.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.2230.21010
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23692
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22010
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2391
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.250
X-RAY DIFFRACTIONr_nbd_other0.2340.2175
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0520.21
X-RAY DIFFRACTIONr_mcbond_it1.0681.0272015
X-RAY DIFFRACTIONr_mcbond_other1.0641.0252014
X-RAY DIFFRACTIONr_mcangle_it1.661.5352523
X-RAY DIFFRACTIONr_mcangle_other1.6611.5372524
X-RAY DIFFRACTIONr_scbond_it1.7341.3632179
X-RAY DIFFRACTIONr_scbond_other1.7061.3342128
X-RAY DIFFRACTIONr_scangle_it2.751.9483182
X-RAY DIFFRACTIONr_scangle_other2.7551.9013105
X-RAY DIFFRACTIONr_lrange_it4.91213.5415021
X-RAY DIFFRACTIONr_lrange_other4.54712.8444864
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69300.2474210X-RAY DIFFRACTION98.021
1.693-1.73900.2254129X-RAY DIFFRACTION98.8982
1.739-1.7900.2084059X-RAY DIFFRACTION99.0967
1.79-1.84500.1843915X-RAY DIFFRACTION99.5423
1.845-1.90500.2043823X-RAY DIFFRACTION99.6351
1.905-1.97200.1893717X-RAY DIFFRACTION99.6515
1.972-2.04600.193558X-RAY DIFFRACTION99.441
2.046-2.1300.1573437X-RAY DIFFRACTION99.6232
2.13-2.22400.1393314X-RAY DIFFRACTION99.7292
2.224-2.33300.1643080X-RAY DIFFRACTION97.4375
2.333-2.45900.153002X-RAY DIFFRACTION99.6349
2.459-2.60800.1632815X-RAY DIFFRACTION97.913
2.608-2.78800.1462653X-RAY DIFFRACTION99.5497
2.788-3.01100.1592499X-RAY DIFFRACTION99.6809
3.011-3.29800.1692258X-RAY DIFFRACTION96.9099
3.298-3.68600.1582069X-RAY DIFFRACTION99.4234
3.686-4.25500.1461838X-RAY DIFFRACTION99.2441
4.255-5.20700.1681560X-RAY DIFFRACTION99.2366
5.207-7.34800.2231204X-RAY DIFFRACTION98.527
7.348-41.6600.194676X-RAY DIFFRACTION96.8481

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