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- PDB-3sng: X-ray structure of fully glycosylated bifunctional nuclease TBN1 ... -

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Basic information

Entry
Database: PDB / ID: 3sng
TitleX-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)
Componentsnuclease
KeywordsHYDROLASE / mainly alpha helical / trinuclear metal centre / bi-functional / endonuclease / 3'-nucleotidase / nucleic acids / mononucleotides / cytosol membrane associated
Function / homology
Function and homology information


Aspergillus nuclease S1 / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Aspergillus nuclease S1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Combination of MAD, Molecular replacement / Resolution: 2.16 Å
AuthorsKoval, T. / Stepankova, A. / Lipovova, P. / Podzimek, T. / Matousek, J. / Duskova, J. / Skalova, T. / Hasek, J. / Dohnalek, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis.
Authors: Koval, T. / Lipovova, P. / Podzimek, T. / Matousek, J. / Duskova, J. / Skalova, T. / Stepankova, A. / Hasek, J. / Dohnalek, J.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,10510
Polymers31,6471
Non-polymers2,4599
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.031, 101.031, 71.529
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-734-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein nuclease


Mass: 31646.535 Da / Num. of mol.: 1 / Fragment: mature enzyme nuclease, UNP residues 26-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Strain: cv. Rutgers / Gene: tbn1 / Plasmid: pLV07 / Production host: Nicotiana benthamiana (plant)
References: UniProt: Q0KFV0, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters

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Sugars , 2 types, 3 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 146 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.0 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 1% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 291 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2010 / Details: 2 mirrors and a double-crystal monochromator
RadiationMonochromator: KMC-1, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.16→35 Å / Num. all: 23089 / Num. obs: 23089 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 11.3 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 26.7
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2280 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXCmodel building
SHELXDphasing
SHELXEmodel building
MOLREPphasing
REFMAC5.6.0060refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCphasing
RefinementMethod to determine structure: Combination of MAD, Molecular replacement
Starting model: PDB ID 1AK0 was used as a model for replacement into initial MAD maps.

1ak0


Resolution: 2.16→35 Å / Cor.coef. Fo:Fc: 0.955 / SU B: 3.011 / SU ML: 0.08 / Isotropic thermal model: isotropic / Cross valid method: Rfree throughout / σ(F): 0
Stereochemistry target values: CCP4 stereochemistry library, version 6.1.3
Details: HYDROGENS HAVE BEEN GENERATED AND USED ONLY IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.22343 1182 5.1 %random
Rwork0.18041 ---
all0.18804 23002 --
obs0.18804 23002 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: 31.642 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.16→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 151 140 2441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212395
X-RAY DIFFRACTIONr_bond_other_d0.0010.021594
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9863263
X-RAY DIFFRACTIONr_angle_other_deg0.9723.0033844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5495266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86624.017117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84315374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6121513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
LS refinement shellResolution: 2.156→2.212 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 95 -
Rwork0.223 1696 -
obs-1696 99.65 %

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