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- PDB-8efg: Crystal structure of human TATDN1 bound to dAMP and two zinc ions -

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Basic information

Entry
Database: PDB / ID: 8efg
TitleCrystal structure of human TATDN1 bound to dAMP and two zinc ions
ComponentsDeoxyribonuclease TATDN1
KeywordsHYDROLASE / Nuclease / TatD / AP-endonuclease / exonuclease
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
TatD deoxyribonuclease family signature 3. / Deoxyribonuclease, TatD-related, conserved site / 3'-5' ssDNA/RNA exonuclease TatD-like / TatD related DNase / Metal-dependent hydrolase
Similarity search - Domain/homology
Chem-3D1 / ADENINE / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyribonuclease TATDN1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDorival, J. / Eichman, B.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1928918 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136401 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity.
Authors: Dorival, J. / Eichman, B.F.
History
DepositionSep 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0May 29, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyribonuclease TATDN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,97512
Polymers33,4041
Non-polymers1,57111
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.880, 76.510, 77.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Deoxyribonuclease TATDN1 / Hepatocarcinoma high expression protein


Mass: 33404.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TATDN1, CDA11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6P1N9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters

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Non-polymers , 7 types, 428 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#7: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.44 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 19% PEG 8000, 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.5→45.3 Å / Num. obs: 52962 / % possible obs: 99.36 % / Redundancy: 6.62 % / Biso Wilson estimate: 21.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 15.93
Reflection shellResolution: 1.505→1.6 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.02 / Num. unique obs: 8656 / CC1/2: 0.84 / Rrim(I) all: 0.743 / % possible all: 92.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XIO

2xio


Resolution: 1.5→45.3 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU R Cruickshank DPI: 0.0681 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 2648 5 %RANDOM
Rwork0.1627 ---
obs0.164 50313 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.84 Å2 / Biso mean: 23.162 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0 Å2
2---0.28 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.5→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 56 417 2806
Biso mean--35.61 39.32 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132524
X-RAY DIFFRACTIONr_bond_other_d0.0340.0152374
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6423411
X-RAY DIFFRACTIONr_angle_other_deg2.2541.5865493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0375306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48823.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57915446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.491513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022817
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02569
LS refinement shellResolution: 1.505→1.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 186 -
Rwork0.282 3536 -
all-3722 -
obs--95.98 %

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