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- PDB-1jy1: CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1) -

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Basic information

Entry
Database: PDB / ID: 1jy1
TitleCRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1)
ComponentsTYROSYL-DNA PHOSPHODIESTERASE
KeywordsHYDROLASE / PLD Superfamily
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 / MAD / Resolution: 1.69 Å
AuthorsDavies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
CitationJournal: Structure / Year: 2002
Title: The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1.
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.
History
DepositionSep 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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


Theoretical massNumber of molelcules
Total (without water)52,8981
Polymers52,8981
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.445, 52.030, 56.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer.

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Components

#1: Protein TYROSYL-DNA PHOSPHODIESTERASE / TDP1


Mass: 52897.582 Da / Num. of mol.: 1 / Fragment: Residues 149-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9NUW8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.6
Details: PEG 8000, sodium chloride, CHES, spermine, pH 9.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1250 mM1dropNaCl
215 mMTris1droppH8.2
31 mMEDTA1drop
42 mMTCEP1drop
55-6 mg/mlprotein1drop
611-15 %PEG80001reservoir
7100 mMCHES1reservoirpH9.6
82-15 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792,0.9794,0.9640
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2001
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.9641
ReflectionResolution: 1.69→30 Å / Num. all: 59625 / Num. obs: 59625 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.48 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 13.42
Reflection shellResolution: 1.69→1.76 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 10.17 / Num. unique all: 5186 / Rsym value: 19.2 / % possible all: 76.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 76.4 %

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.69→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: refmac5
RfactorNum. reflectionSelection details
Rfree0.229 3349 random
Rwork0.198 --
all0.198 66989 -
obs0.198 66989 -
Refinement stepCycle: LAST / Resolution: 1.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 0 345 3850
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d1.813
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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