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- PDB-5fbd: S1 nuclease from Aspergillus oryzae in complex with phosphate and... -

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Basic information

Entry
Database: PDB / ID: 5fbd
TitleS1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine
ComponentsNuclease S1
KeywordsHYDROLASE / Endonuclease / Zinc dependent / Complex
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 / PHOSPHATE ION / Nuclease S1
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / 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 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8237
Polymers29,0841
Non-polymers7406
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-119 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.040, 62.426, 84.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 29083.660 Da / Num. of mol.: 1
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.: 1
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 , 4 types, 382 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C9H13N3O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 1.95 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1 M Citric acid pH 3.8, 25% w/v Polyethylene glycol 3,350
Temp details: stable

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.75→30.08 Å / Num. obs: 22221 / % possible obs: 95.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 5.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.1 / % possible all: 72.2

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Processing

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

Resolution: 1.75→30.08 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 2.212 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21159 1138 5.1 %Random selection
Rwork0.1515 ---
obs0.15288 22191 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2---0.84 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 38 377 2464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192190
X-RAY DIFFRACTIONr_bond_other_d0.0060.021921
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.942996
X-RAY DIFFRACTIONr_angle_other_deg1.134467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50726.132106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17515338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.895153
X-RAY DIFFRACTIONr_chiral_restr0.1190.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022529
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02476
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_it0.881.0181067
X-RAY DIFFRACTIONr_mcbond_other0.8731.0151066
X-RAY DIFFRACTIONr_mcangle_it1.3611.5221332
X-RAY DIFFRACTIONr_mcangle_other1.3631.5251333
X-RAY DIFFRACTIONr_scbond_it1.3181.1491123
X-RAY DIFFRACTIONr_scbond_other1.3171.151124
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.991.6811665
X-RAY DIFFRACTIONr_long_range_B_refined4.7539.9163003
X-RAY DIFFRACTIONr_long_range_B_other4.2989.1132810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å
RfactorNum. reflection% reflection
Rfree0.281 59 4.7 %
Rwork0.214 1203 -
obs--73.63 %

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