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- PDB-1q32: Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase -

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Basic information

Entry
Database: PDB / ID: 1q32
TitleCrystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase
Componentstyrosyl-DNA phosphodiesterase
KeywordsREPLICATION / TRANSCRIPTION / HYDROLASE / Tyrosyl-DNA Phosphodiesterase / TDP / DNA repair
Function / homology
Function and homology information


5'-tyrosyl-DNA phosphodiesterase activity / 3'-tyrosyl-DNA phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / single-stranded DNA binding / double-stranded DNA binding / DNA repair / mitochondrion / nucleus
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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.03 Å
AuthorsHe, X. / Babaoglu, K. / Price, A. / Nitiss, K.C. / Nitiss, J.L. / White, S.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison
Authors: He, X. / van Waardenburg, R.C. / Babaoglu, K. / Price, A.C. / Nitiss, K.C. / Nitiss, J.L. / Bjornsti, M.A. / White, S.W.
History
DepositionJul 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tyrosyl-DNA phosphodiesterase
B: tyrosyl-DNA phosphodiesterase
C: tyrosyl-DNA phosphodiesterase
D: tyrosyl-DNA phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)249,6564
Polymers249,6564
Non-polymers00
Water15,529862
1
A: tyrosyl-DNA phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)62,4141
Polymers62,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tyrosyl-DNA phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)62,4141
Polymers62,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tyrosyl-DNA phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)62,4141
Polymers62,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: tyrosyl-DNA phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)62,4141
Polymers62,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.163, 82.207, 98.442
Angle α, β, γ (deg.)89.39, 85.81, 67.12
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
DetailsThere are 4 biological assemblies in the asymmetric unit. Each is a monomer, labeled A, B, C, or D.

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Components

#1: Protein
tyrosyl-DNA phosphodiesterase / E.C.3.1.4.- / Tyrosine-DNA Phosphodiesterase / Tdp1p / Hypothetical 62.3 kDa protein in FAT2-MCX1 intergenic region


Mass: 62414.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TDP1 / Plasmid: pET-23b (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: P38319, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7.8
Details: PEG 4000, Hepes, LiSO4, DTT, 1.6.Hexanediol , pH 7.8, EVAPORATION, temperature 291.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12B10.9789, 0.9796, 0.9637
SYNCHROTRONAPS 22-ID21.02466
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 24, 2001
MARRESEARCH2CCDDec 11, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si (220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97961
30.96371
41.024661
ReflectionResolution: 1.8→50 Å / Num. all: 155815 / Num. obs: 155815 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.8→1.86 Å / % possible all: 54.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.03→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2414 10979 RANDOM
Rwork0.2141 --
all0.21411 110179 -
obs0.21411 110179 -
Refinement stepCycle: LAST / Resolution: 2.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13656 0 0 862 14518
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.4441.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it1.9542
X-RAY DIFFRACTIONc_scangle_it2.9372.5

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