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- PDB-9emg: SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with... -

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Basic information

Entry
Database: PDB / ID: 9emg
TitleSmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-5'-monophosphate as a product of c-di-GMP cleavage
ComponentsS1/P1 nuclease
KeywordsHYDROLASE / Nuclease
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.148 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.02.1.01/0.0/18_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
DepositionMar 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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)58,52020
Polymers56,7102
Non-polymers1,81118
Water13,457747
1
A: S1/P1 nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,13010
Polymers28,3551
Non-polymers7759
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1/P1 nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,39110
Polymers28,3551
Non-polymers1,0369
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.340, 72.637, 82.940
Angle α, β, γ (deg.)90.000, 102.098, 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: FEO86_17535, HKK60_04680, I5U85_21415 / Plasmid: pET303/CT-His_SmNuc1 / Details (production host): MalE signal peptide / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6C8X1V5

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Non-polymers , 6 types, 765 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
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 5000. Protein concentration 7.5 mg/ml. Cryo-protection by glycerol 25 % 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: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.148→43.393 Å / Num. obs: 165597 / % possible obs: 96.8 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.054 / Net I/σ(I): 18.5
Reflection shellResolution: 1.148→1.182 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 8280 / CC1/2: 0.824 / Rrim(I) all: 0.701

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.148→43.393 Å / Cor.coef. Fo:Fc: 0.983 / SU B: 0.842 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.027
Details: Hydrogens have been added in their riding positions. The last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflection
Rfree0.1311 7969 5 %
Rwork0.1107 165597 -
all0.113 --
obs0.1129 165597 90.609 %
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: 15.231 Å2
Baniso -1Baniso -2Baniso -3
1-0.218 Å20 Å20.075 Å2
2---0.319 Å2-0 Å2
3---0.063 Å2
Refinement stepCycle: LAST / Resolution: 1.148→43.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 90 747 4709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134354
X-RAY DIFFRACTIONr_bond_other_d0.0070.0154100
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.6465967
X-RAY DIFFRACTIONr_angle_other_deg1.5791.5929432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98420.986284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02715743
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg15.08154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4641551
X-RAY DIFFRACTIONr_chiral_restr0.1040.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021104
X-RAY DIFFRACTIONr_nbd_refined0.230.21014
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23909
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22078
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2484
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.250
X-RAY DIFFRACTIONr_nbd_other0.2310.2135
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2420.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1070.21
X-RAY DIFFRACTIONr_mcbond_it1.441.2272082
X-RAY DIFFRACTIONr_mcbond_other1.426259.0162081
X-RAY DIFFRACTIONr_mcangle_it1.7991.8532624
X-RAY DIFFRACTIONr_mcangle_other1.79923.1762625
X-RAY DIFFRACTIONr_scbond_it2.2281.5762272
X-RAY DIFFRACTIONr_scbond_other2.2188.2472244
X-RAY DIFFRACTIONr_scangle_it2.6792.2543300
X-RAY DIFFRACTIONr_scangle_other2.6542.2283259
X-RAY DIFFRACTIONr_lrange_it3.5899999.9995354
X-RAY DIFFRACTIONr_lrange_other2.7689999.9995110
X-RAY DIFFRACTIONr_rigid_bond_restr2.23734346
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.148-1.17800.2127305X-RAY DIFFRACTION54.2236
1.178-1.21100.1759239X-RAY DIFFRACTION70.4299
1.211-1.24600.18410046X-RAY DIFFRACTION78.7613
1.246-1.28400.18610435X-RAY DIFFRACTION84.2347
1.284-1.32600.16910806X-RAY DIFFRACTION89.6615
1.326-1.37300.14911254X-RAY DIFFRACTION96.5594
1.373-1.42400.13311168X-RAY DIFFRACTION99.3241
1.424-1.48300.12610784X-RAY DIFFRACTION99.5201
1.483-1.54800.10610232X-RAY DIFFRACTION98.6597
1.548-1.62400.0839869X-RAY DIFFRACTION99.9392
1.624-1.71200.0719421X-RAY DIFFRACTION99.6088
1.712-1.81600.0698891X-RAY DIFFRACTION99.5967
1.816-1.94100.0818278X-RAY DIFFRACTION98.5593
1.941-2.09600.087766X-RAY DIFFRACTION99.5386
2.096-2.29600.087216X-RAY DIFFRACTION99.6823
2.296-2.56700.0836470X-RAY DIFFRACTION99.2636
2.567-2.96400.0965689X-RAY DIFFRACTION98.4426
2.964-3.62900.1094865X-RAY DIFFRACTION99.6518
3.629-5.12600.123752X-RAY DIFFRACTION98.9712
5.126-43.39300.2152111X-RAY DIFFRACTION98.3691
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02420.0027-0.00720.01050.00440.0110.0001-0.0002-0.00150.0003-0.0007-0.00070.00110.00050.00060.00560.0002-00.0071-0.00010.006318.08374.472639.6643
20.0185-0.0083-0.0360.0859-0.0180.09180.00360.00020.0015-0.0314-0.0011-0.01050.0024-0.0006-0.00260.0181-0.00040.00490.0072-0.00060.0112-0.263-4.85055.1849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALL{ A|27-277 }A27 - 277
2X-RAY DIFFRACTION2ALL{ B|27-271 }B27 - 271

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