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- PDB-1mu9: Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)... -

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Basic information

Entry
Database: PDB / ID: 1mu9
TitleCrystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex
ComponentsTyrosyl-DNA Phosphodiesterase
KeywordsHYDROLASE / PLD Superfamily / Protein-Vanadate Complex
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 / DNA repair / intracellular membrane-bounded organelle ...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 / DNA repair / intracellular membrane-bounded organelle / 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
VANADATE ION / : / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDavies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Insights Into Substrate Binding and Catalytic Mechanism of Human Tyrosyl-DNA Phosphodiesterase (Tdp1) from Vanadate- and Tungstate-Inhibited Structures
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
#1: Journal: 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.J.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-DNA Phosphodiesterase
B: Tyrosyl-DNA Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8766
Polymers109,4622
Non-polymers4144
Water5,098283
1
A: Tyrosyl-DNA Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9383
Polymers54,7311
Non-polymers2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9383
Polymers54,7311
Non-polymers2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.028, 104.980, 194.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer. There are two monomers per asymmetric unit, with the A monomer having the higher occupancy of bound vanadate

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Components

#1: Protein Tyrosyl-DNA Phosphodiesterase / TDP1


Mass: 54731.195 Da / Num. of mol.: 2 / Fragment: RESIDUES 149-608 / Mutation: D322N,M328T,F548L
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: GenBank: 20127586, UniProt: Q9NUW8*PLUS
#2: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: PEG 8000, sodium chloride, HEPES, spermine, pH 7.8, 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 mMTris-HCl1droppH8.2
31 mMEDTA1drop
42 mMTCEP1drop
56.5 mg/mlprotein1drop
65 mMsodium orthovanadate1reservoir
719-21 %PEG30001reservoir
8100 mMHEPES1reservoirpH7.8
9200 mM1reservoirNaCl
1010-15 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.4 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 2.05→19.97 Å / Num. obs: 66910 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.62 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.78
Reflection shellResolution: 2.05→2.12 Å / Rsym value: 0.387 / % possible all: 100
Reflection
*PLUS
Num. obs: 65167
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.387

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jy1

1jy1


Resolution: 2.05→19.97 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The density is better defined for bound vanadate in the A subunit.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3563 -random
Rwork0.199 ---
all0.205 65032 --
obs0.205 65032 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.05→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6845 0 18 283 7146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.618
X-RAY DIFFRACTIONr_chiral_restr0.115
Refinement
*PLUS
Lowest resolution: 100 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.618

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