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- PDB-7qtb: S1 nuclease from Aspergillus oryzae in complex with cytidine-5'-m... -

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Basic information

Entry
Database: PDB / ID: 7qtb
TitleS1 nuclease from Aspergillus oryzae in complex with cytidine-5'-monophosphate
ComponentsNuclease S1
KeywordsHYDROLASE / nuclease / complex / nucleotide / 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
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Nuclease S1
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 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)61,31825
Polymers58,1672
Non-polymers3,15123
Water16,177898
1
A: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,63912
Polymers29,0841
Non-polymers1,55511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,67913
Polymers29,0841
Non-polymers1,59612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.075, 48.459, 65.547
Angle α, β, γ (deg.)107.470, 90.076, 105.702
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, 917 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-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#6: 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.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
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: 1.04→44.358 Å / Num. obs: 196791 / % possible obs: 84.5 % / Observed criterion σ(I): -3.7 / Redundancy: 3.6 % / Biso Wilson estimate: 6.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Net I/σ(I): 10.8
Reflection shellResolution: 1.04→1.06 Å / Num. unique obs: 4899 / CC1/2: 0.829 / Rrim(I) all: 0.505 / % possible all: 42.2

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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: 1.04→44.358 Å / Cor.coef. Fo:Fc: 0.984 / SU B: 0.575 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.024
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
Rfree0.1307 9747 5 %Random
Rwork0.1087 196789 --
all0.11 ---
obs0.1097 196789 84.456 %-
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: 11.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.041 Å2-0.043 Å20.01 Å2
2--0.024 Å2-0.048 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.04→44.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 175 898 5148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134840
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154162
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.6646695
X-RAY DIFFRACTIONr_angle_other_deg1.7171.6079735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44625.556234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80215709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.625156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2669
X-RAY DIFFRACTIONr_chiral_restr_other0.0350.22
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026043
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021056
X-RAY DIFFRACTIONr_nbd_refined0.2290.21190
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.24023
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22276
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2575
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.226
X-RAY DIFFRACTIONr_nbd_other0.2020.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.286
X-RAY DIFFRACTIONr_mcbond_it0.8320.9412317
X-RAY DIFFRACTIONr_mcbond_other0.843617.7452316
X-RAY DIFFRACTIONr_mcangle_it1.031.4232924
X-RAY DIFFRACTIONr_mcangle_other1.0398.7692925
X-RAY DIFFRACTIONr_scbond_it1.5141.1332523
X-RAY DIFFRACTIONr_scangle_it1.6871.6443731
X-RAY DIFFRACTIONr_scangle_other1.6871.6453732
X-RAY DIFFRACTIONr_rigid_bond_restr2.57434801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.0670.223770.2027456X-RAY DIFFRACTION45.5301
1.067-1.09600.18312138X-RAY DIFFRACTION72.0057
1.096-1.12800.15314096X-RAY DIFFRACTION85.8779
1.128-1.16300.13913468X-RAY DIFFRACTION85.3053
1.163-1.20100.12513076X-RAY DIFFRACTION84.9532
1.201-1.24300.10713060X-RAY DIFFRACTION87.6981
1.243-1.2900.10212559X-RAY DIFFRACTION87.623
1.29-1.34300.09511852X-RAY DIFFRACTION85.6297
1.343-1.40200.08211922X-RAY DIFFRACTION90.3182
1.402-1.47100.07811457X-RAY DIFFRACTION90.3264
1.471-1.5500.07410795X-RAY DIFFRACTION89.7415
1.55-1.64400.07110043X-RAY DIFFRACTION88.2358
1.644-1.75700.0769952X-RAY DIFFRACTION93.1573
1.757-1.89800.0879253X-RAY DIFFRACTION92.7154
1.898-2.07900.1038396X-RAY DIFFRACTION91.6594
2.079-2.32400.17409X-RAY DIFFRACTION89.5023
2.324-2.68300.1096966X-RAY DIFFRACTION94.8659
2.683-3.28500.1225745X-RAY DIFFRACTION93.1873
3.285-4.63900.1254248X-RAY DIFFRACTION89.2625
4.639-44.35800.1952522X-RAY DIFFRACTION96.1128

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