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- PDB-5fbg: S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with... -

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Basic information

Entry
Database: PDB / ID: 5fbg
TitleS1 nuclease from Aspergillus oryzae, mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine.
ComponentsNuclease S1
KeywordsHYDROLASE / Endonuclease / Zinc dependent / Complex / mutant
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 / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / Peptidase S8, subtilisin, Asp-active site / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYCYTIDINE / 2'-DEOXY-GUANOSINE / PHOSPHATE ION / Nuclease S1
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKoval, T. / Oestergaard, L.H. / Dohnalek, J.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLG14009 Czech Republic
BIOCEV: Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University from the European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
European Community283570/8787
CitationJournal: PLoS ONE / Year: 2016
Title: Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
Authors: Koval, T. / stergaard, L.H. / Lehmbeck, J. / Nrgaard, A. / Lipovova, P. / Duskova, J. / Skalova, T. / Trundova, M. / Kolenko, P. / Fejfarova, K. / Stransky, J. / Svecova, L. / Hasek, J. / Dohnalek, J.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jul 29, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,35417
Polymers58,1652
Non-polymers2,18915
Water11,746652
1
A: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2719
Polymers29,0831
Non-polymers1,1888
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclease S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0848
Polymers29,0831
Non-polymers1,0017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.760, 106.760, 127.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1193-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 21 - 284 / Label seq-ID: 1 - 264

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 29082.676 Da / Num. of mol.: 2 / Mutation: D65N
Source method: isolated from a genetically manipulated source
Details: Mature protein without signal sequence. / Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / 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: isolated from a genetically manipulated source
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 , 5 types, 663 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
#5: Chemical ChemComp-DCZ / 2'-DEOXYCYTIDINE


Type: DNA OH 5 prime terminus / Mass: 227.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O4
#6: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Temp details: stable

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.97→37.47 Å / Num. obs: 59852 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.3
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: our previous model of S1

Resolution: 1.97→37.47 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 2.655 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18705 3024 5.1 %Random selection
Rwork0.1579 ---
obs0.15889 59809 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.934 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.97→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 123 652 4859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194387
X-RAY DIFFRACTIONr_bond_other_d0.0090.023816
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9426018
X-RAY DIFFRACTIONr_angle_other_deg1.4833.0018850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27626.039207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46515645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.605156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025215
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02979
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5871.9712149
X-RAY DIFFRACTIONr_mcbond_other1.581.9692148
X-RAY DIFFRACTIONr_mcangle_it2.2612.9472689
X-RAY DIFFRACTIONr_mcangle_other2.2612.952690
X-RAY DIFFRACTIONr_scbond_it2.3562.2722238
X-RAY DIFFRACTIONr_scbond_other2.3552.2742239
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6563.3243321
X-RAY DIFFRACTIONr_long_range_B_refined6.25218.0285840
X-RAY DIFFRACTIONr_long_range_B_other5.64417.1825522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 31476 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.97→2.021 Å
RfactorNum. reflection% reflection
Rfree0.263 200 4.7 %
Rwork0.264 4071 -
obs--97.65 %

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