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- PDB-4p5u: Crystal structure of TatD -

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Basic information

Entry
Database: PDB / ID: 4p5u
TitleCrystal structure of TatD
ComponentsTat-linked quality control protein TatD
KeywordsHYDROLASE / DNA repair / DNA processing / exonuclease / TIM barrel
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
3'-5' ssDNA/RNA exonuclease TatD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMar 20, 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: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
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_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
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


Theoretical massNumber of molelcules
Total (without water)29,2481
Polymers29,2481
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.165, 52.697, 98.363
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: 29248.182 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.91 Å3/Da / Density % sol: 35.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium citrate dibasic, 20% PEG3350

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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: Dec 13, 2010
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→30 Å / Num. obs: 15670 / % possible obs: 98.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.078 / Χ2: 1.134 / Net I/av σ(I): 23.163 / Net I/σ(I): 9.3 / Num. measured all: 90131
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.035.90.3537820.894100
2.03-2.0760.3097810.902100
2.07-2.1160.2747560.912100
2.11-2.1560.2277860.892100
2.15-2.25.90.2097730.916100
2.2-2.2550.1966591.6384.7
2.25-2.314.90.2227181.61892.9
2.31-2.3760.167840.921100
2.37-2.445.90.1347790.931100
2.44-2.525.90.1418011.031100
2.52-2.615.90.127651.034100
2.61-2.715.90.1127961.124100
2.71-2.845.90.0997831.30699.9
2.84-2.995.80.0887921.42899.9
2.99-3.175.80.0787891.42100
3.17-3.425.80.0558061.23899.8
3.42-3.765.30.057921.48298.8
3.76-4.315.60.0388161.187100
4.31-5.425.80.0348281.047100
5.42-305.40.0318841.10899.3

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Processing

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

1xwy


Resolution: 2→23.395 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1549 9.98 %
Rwork0.2029 13976 -
obs0.2071 15525 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.53 Å2 / Biso mean: 22.0987 Å2 / Biso min: 9.59 Å2
Refinement stepCycle: final / Resolution: 2→23.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 219 2273
Biso mean---27.59 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042103
X-RAY DIFFRACTIONf_angle_d0.9752862
X-RAY DIFFRACTIONf_chiral_restr0.057318
X-RAY DIFFRACTIONf_plane_restr0.005378
X-RAY DIFFRACTIONf_dihedral_angle_d15.553766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.06080.28051390.22031259139898
2.0608-2.13440.26931400.217512531393100
2.1344-2.21980.24231390.221512641403100
2.2198-2.32080.36991130.33141034114781
2.3208-2.4430.27631420.209812891431100
2.443-2.59590.26331430.206312831426100
2.5959-2.7960.23891420.202712811423100
2.796-3.07680.25041450.221113081453100
3.0768-3.52070.19861440.188912981442100
3.5207-4.43080.21041460.16821310145699
4.4308-23.39690.21921560.17813971553100

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