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- PDB-3sq5: Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodieste... -

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Basic information

Entry
Database: PDB / ID: 3sq5
TitleCrystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE / Phosphodiesterase / DNA Binding / NUCLEAR
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGajewski, S. / White, S.W.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily.
Authors: Gajewski, S. / Comeaux, E.Q. / Jafari, N. / Bharatham, N. / Bashford, D. / White, S.W. / van Waardenburg, R.C.
History
DepositionJul 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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
C: Tyrosyl-DNA phosphodiesterase 1
D: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)216,1124
Polymers216,1124
Non-polymers00
Water2,252125
1
A: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)54,0281
Polymers54,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)54,0281
Polymers54,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)54,0281
Polymers54,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)54,0281
Polymers54,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Tyrosyl-DNA phosphodiesterase 1
B: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)108,0562
Polymers108,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-6 kcal/mol
Surface area34440 Å2
MethodPISA
6
C: Tyrosyl-DNA phosphodiesterase 1

D: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)108,0562
Polymers108,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1630 Å2
ΔGint-5 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.453, 82.036, 98.677
Angle α, β, γ (deg.)89.80, 94.33, 112.78
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A79 - 543
2112B79 - 543
3112C79 - 543
4112D79 - 543

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Components

#1: Protein
Tyrosyl-DNA phosphodiesterase 1 / Tyr-DNA phosphodiesterase 1


Mass: 54027.977 Da / Num. of mol.: 4 / Fragment: unp residues 79-539 / Mutation: H432N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TDP1, YBR223C, YBR1520 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P38319, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 291 K / pH: 7.8
Details: 20% PEG3350, 0.1M HEPES, 0.2M magnesium sulfate, 5mM TCEP, 3% Hexanediol-1,6, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2008
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 75956 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.241 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q32

1q32


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 15.36 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3872 4.9 %RANDOM
Rwork0.203 ---
obs0.204 75448 96.1 %-
all-75448 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0.97 Å21.22 Å2
2---2.32 Å2-1.26 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13657 0 0 125 13782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02214033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9618983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01351657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84623.659615
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.404152488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9581568
X-RAY DIFFRACTIONr_chiral_restr0.1340.22113
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110391
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9611.58422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.818213722
X-RAY DIFFRACTIONr_scbond_it2.82335611
X-RAY DIFFRACTIONr_scangle_it4.5354.55261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1650tight positional0.070.05
2B1650tight positional0.070.05
3C1650tight positional0.060.05
4D1650tight positional0.060.05
1A1705medium positional0.080.5
2B1705medium positional0.080.5
3C1705medium positional0.070.5
4D1705medium positional0.070.5
1A1650tight thermal0.280.5
2B1650tight thermal0.250.5
3C1650tight thermal0.230.5
4D1650tight thermal0.220.5
1A1705medium thermal0.282
2B1705medium thermal0.262
3C1705medium thermal0.242
4D1705medium thermal0.232
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 291 -
Rwork0.234 5619 -
obs--96.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.50070.2165-0.38381.33190.29141.15450.03130.0053-0.09660.0317-0.0296-0.01790.08310.0671-0.00170.14690.088-0.13180.2544-0.04110.1306-9.97532.873-3.188
22.19160.0457-0.13811.64920.18091.12720.06510.11560.14230.07230.015-0.0423-0.06860.0605-0.08020.18820.0586-0.09740.2911-0.03260.0858-24.10965.44418.896
31.6155-0.30540.50712.62570.61742.19750.17170.01280.1543-0.3437-0.0781-0.2642-0.3362-0.0632-0.09360.17850.06140.03970.23040.04750.1924-10.35522.65345.973
41.9684-0.71620.43342.4411-0.38921.2663-0.04370.03850.00670.2150.0604-0.04380.04850.1155-0.01680.240.0285-0.10410.28650.04230.124-30.05964.99867.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 538
2X-RAY DIFFRACTION2B79 - 538
3X-RAY DIFFRACTION3C79 - 538
4X-RAY DIFFRACTION4D79 - 538

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