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- PDB-4pe8: Crystal structure of TatD in complex with trinucleotide DNA -

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Basic information

Entry
Database: PDB / ID: 4pe8
TitleCrystal structure of TatD in complex with trinucleotide DNA
Components
  • DNA (5'-D(*GP*CP*T)-3')
  • Tat-linked quality control protein TatD
KeywordsHYDROLASE/DNA / DNA repair / DNA processing / exonuclease / TIM barrel / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA nuclease activity / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / response to hydrogen peroxide / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / magnesium ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
3'-5' ssDNA/RNA exonuclease TatD / TatD deoxyribonuclease family signature 2. / TatD deoxyribonuclease family signature 3. / Deoxyribonuclease, TatD-related, conserved site / 3'-5' ssDNA/RNA exonuclease TatD-like / TatD related DNase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DNA / 3'-5' ssDNA/RNA exonuclease TatD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.894 Å
AuthorsChen, Y. / Li, C.-L. / Hsiao, Y.-Y. / Duh, Y. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure and function of TatD exonuclease in DNA repair.
Authors: Chen, Y.C. / Li, C.L. / Hsiao, Y.Y. / Duh, Y. / Yuan, H.S.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tat-linked quality control protein TatD
B: DNA (5'-D(*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)29,8842
Polymers29,8842
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-1 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.450, 52.871, 101.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tat-linked quality control protein TatD / Deoxyribonuclease TatD / DNase TatD


Mass: 29005.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tatD, mttC, yigW, yigX, b4483, JW5931 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P27859, Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*GP*CP*T)-3')


Mass: 877.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4% Tacsimate pH 4 and 12% PEG3350 / PH range: 4 - 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2011
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.894→30 Å / Num. obs: 5539 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.117 / Χ2: 1.477 / Net I/av σ(I): 17.947 / Net I/σ(I): 7.8 / Num. measured all: 30630
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.894-35.50.4285351.24299.6
3-3.125.40.3695451.31599.5
3.12-3.275.70.2765341.442100
3.27-3.445.60.215401.58999.6
3.44-3.655.30.1795381.65298.2
3.65-3.935.50.125531.39899.6
3.93-4.335.70.0915481.38999.6
4.33-4.955.70.0865641.999.6
4.95-6.235.70.0835681.49899.6
6.23-305.30.0396141.32498.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXphasing
Cootmodel building
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWY

1xwy


Resolution: 2.894→28.419 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 550 9.98 %Random selection
Rwork0.1945 4963 --
obs0.1993 5513 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.35 Å2 / Biso mean: 41.1529 Å2 / Biso min: 23.26 Å2
Refinement stepCycle: final / Resolution: 2.894→28.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 58 0 39 2135
Biso mean---36.69 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032159
X-RAY DIFFRACTIONf_angle_d0.7182950
X-RAY DIFFRACTIONf_chiral_restr0.048327
X-RAY DIFFRACTIONf_plane_restr0.003380
X-RAY DIFFRACTIONf_dihedral_angle_d14.901789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.894-3.18480.33061320.24381200133299
3.1848-3.64480.28611360.19981214135099
3.6448-4.5890.18781370.176412411378100
4.589-28.42080.22321450.18731308145399

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