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- PDB-1qzq: human Tyrosyl DNA phosphodiesterase -

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Basic information

Entry
Database: PDB / ID: 1qzq
Titlehuman Tyrosyl DNA phosphodiesterase
Componentstyrosyl-DNA phosphodiesterase 1
Keywordshydrolase / DNA binding protein / DNA Repair / replication
Function / homology
Function and homology information


3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair ...3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tyrosyl-DNA phosphodiesterase I / Tyrosyl-DNA phosphodiesterase / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRaymond, A.C. / Rideout, M.C. / Staker, B. / Hjerrild, K. / Burgin Jr., A.B.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Analysis of Human Tyrosyl-DNA Phosphodiesterase I Catalytic Residues.
Authors: Raymond, A.C. / Rideout, M.C. / Staker, B. / Hjerrild, K. / Burgin Jr., A.B.
History
DepositionSep 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tyrosyl-DNA phosphodiesterase 1
B: tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)109,8392
Polymers109,8392
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.024, 105.131, 194.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tyrosyl-DNA phosphodiesterase 1


Mass: 54919.340 Da / Num. of mol.: 2 / Fragment: residues 149-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: tdp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NUW8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.4
Details: PEG 8000, CHES, 8mM spermine, pH 9.4, VAPOR DIFFUSION, SITTING DROP, temperature 16K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 40794 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 0.097 / Net I/σ(I): 18.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 6326 / Rsym value: 0.403

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Processing

Software
NameVersionClassification
CNX2002refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.54 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2371494.44 / Data cutoff high rms absF: 2371494.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2067 5.1 %RANDOM
Rwork0.185 ---
obs-40794 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.301 Å2 / ksol: 0.367093 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å20 Å2
2--7.24 Å20 Å2
3----3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 0 238 7250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 337 5.1 %
Rwork0.226 6326 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARWATER.TOP

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