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- PDB-7qta: S1 nuclease from Aspergillus oryzae in complex with uridine -

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Basic information

Entry
Database: PDB / ID: 7qta
TitleS1 nuclease from Aspergillus oryzae in complex with uridine
ComponentsNuclease S1
KeywordsHYDROLASE / Nuclease / Complex / Nucleoside / Lattice translocation defect
Function / homology
Function and homology information


Aspergillus nuclease S1 / nuclease activity / DNA catabolic process / endonuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function
S1/P1 nuclease / S1/P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / Peptidase S8, subtilisin, Asp-active site
Similarity search - Domain/homology
PHOSPHATE ION / URIDINE / Nuclease S1
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsAdamkova, K. / Koval, T. / Kolenko, P. / Oestergaard, L.H. / Dohnalek, J.
Funding supportEuropean Union, 4items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127European Union
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447European Union
Czech Science Foundation20-12109SEuropean Union
European Regional Development FundCZ.02.1.01/0.0/0.0/18_046/0015974European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.
Authors: Adamkova, K. / Koval', T. / Ostergaard, L.H. / Duskova, J. / Maly, M. / Svecova, L. / Skalova, T. / Kolenko, P. / Dohnalek, J.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclease S1
B: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56419
Polymers58,1672
Non-polymers2,39717
Water13,872770
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A: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0849
Polymers29,0841
Non-polymers1,0018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,48010
Polymers29,0841
Non-polymers1,3969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.040, 48.186, 65.232
Angle α, β, γ (deg.)107.184, 90.114, 105.618
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Nuclease S1 / Deoxyribonuclease S1 / Endonuclease S1 / Single-stranded-nucleate endonuclease


Mass: 29083.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: ATCC 42149 / RIB 40 / Gene: nucS, AO090001000075 / Production host: Aspergillus oryzae (mold) / References: UniProt: P24021, Aspergillus nuclease S1
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 783 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, protein concentration 10 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.06→44.2 Å / Num. obs: 187610 / % possible obs: 86.02 % / Observed criterion σ(I): -3.7 / Redundancy: 3.6 % / Biso Wilson estimate: 9.8 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.085 / Net I/σ(I): 8
Reflection shellResolution: 1.06→1.088 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 10422 / CC1/2: 0.373 / Rrim(I) all: 1.145 / % possible all: 64.47

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FB9

5fb9


Resolution: 1.06→44.2 Å / Cor.coef. Fo:Fc: 0.984 / SU B: 0.684 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.026
Details: Hydrogens have been added in their riding positions. Structure factors were corrected for lattice translocation defect. Last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.1468 9423 5 %Random
Rwork0.1181 187575 --
all0.12 ---
obs0.1205 187610 86.015 %-
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: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.498 Å2-0.01 Å2-0.011 Å2
2--0.272 Å20.095 Å2
3---0.097 Å2
Refinement stepCycle: LAST / Resolution: 1.06→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 135 770 4980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134684
X-RAY DIFFRACTIONr_bond_other_d0.0090.0164042
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.6546495
X-RAY DIFFRACTIONr_angle_other_deg1.7161.5989463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33925.467225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12815706
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg4.494158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.861156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021022
X-RAY DIFFRACTIONr_nbd_refined0.2330.21201
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.24026
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22349
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21944
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2471
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.228
X-RAY DIFFRACTIONr_nbd_other0.2070.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.263
X-RAY DIFFRACTIONr_mcbond_it1.0471.1972260
X-RAY DIFFRACTIONr_mcbond_other1.0312.5412259
X-RAY DIFFRACTIONr_mcangle_it1.2951.8092858
X-RAY DIFFRACTIONr_mcangle_other1.30811.6012859
X-RAY DIFFRACTIONr_scbond_it1.671.3932424
X-RAY DIFFRACTIONr_scangle_it1.9142.0263588
X-RAY DIFFRACTIONr_scangle_other1.9142.0263589
X-RAY DIFFRACTIONr_rigid_bond_restr2.49534684
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.08800.2910419X-RAY DIFFRACTION64.4541
1.088-1.11700.24913329X-RAY DIFFRACTION84.7793
1.117-1.1500.21513030X-RAY DIFFRACTION85.0189
1.15-1.18500.1912375X-RAY DIFFRACTION83.3614
1.185-1.22400.1512540X-RAY DIFFRACTION87.2045
1.224-1.26700.13612099X-RAY DIFFRACTION86.9368
1.267-1.31500.12211648X-RAY DIFFRACTION86.6989
1.315-1.36800.10711369X-RAY DIFFRACTION87.9205
1.368-1.42900.09111127X-RAY DIFFRACTION89.7339
1.429-1.49900.08110683X-RAY DIFFRACTION90.2509
1.499-1.5800.0769971X-RAY DIFFRACTION88.6469
1.58-1.67600.0739598X-RAY DIFFRACTION89.8101
1.676-1.79100.0839215X-RAY DIFFRACTION92.0855
1.791-1.93500.1018480X-RAY DIFFRACTION91.3301
1.935-2.11900.1077610X-RAY DIFFRACTION88.6327
2.119-2.36900.116791X-RAY DIFFRACTION87.1535
2.369-2.73500.1176068X-RAY DIFFRACTION89.065
2.735-3.34800.1275043X-RAY DIFFRACTION87.4155
3.348-4.72700.1193881X-RAY DIFFRACTION86.8427
4.727-44.200.172300X-RAY DIFFRACTION93.4959

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