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- PDB-3sq7: Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodieste... -

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Basic information

Entry
Database: PDB / ID: 3sq7
TitleCrystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N_Glu 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 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 5, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,74811
Polymers216,0764
Non-polymers6727
Water13,403744
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4035
Polymers54,0191
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1152
Polymers54,0191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)54,0191
Polymers54,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2113
Polymers54,0191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Tyrosyl-DNA phosphodiesterase 1
D: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6148
Polymers108,0382
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-59 kcal/mol
Surface area34020 Å2
MethodPISA
6
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules

C: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)108,1343
Polymers108,0382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area4260 Å2
ΔGint-44 kcal/mol
Surface area33900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.350, 82.190, 99.290
Angle α, β, γ (deg.)86.79, 85.57, 66.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 79 - 543 / Label seq-ID: 2 - 466

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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


Mass: 54018.945 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 44.55 %
Crystal growTemperature: 291 K / pH: 7.8
Details: 17% PEG3350, 0.1M HEPES, 0.2M magnesium sulfate, 5mM TCEP, 5% 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-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2007
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 119602 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.6 / % possible all: 81.3

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Processing

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

1q32


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.821 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 6070 5 %RANDOM
Rwork0.174 ---
obs0.176 115913 97.2 %-
all-115913 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20.86 Å2-0.05 Å2
2---0.05 Å20.36 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13884 0 35 744 14663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02214336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.95919423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8351710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76923.786626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.001152524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.221563
X-RAY DIFFRACTIONr_chiral_restr0.1440.22164
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110615
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_it1.9881.58611
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.465214026
X-RAY DIFFRACTIONr_scbond_it3.8735725
X-RAY DIFFRACTIONr_scangle_it6.3044.55386
X-RAY DIFFRACTIONr_rigid_bond_restr2.405314332
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
1A1674tight positional0.070.05
2B1674tight positional0.080.05
3C1674tight positional0.070.05
4D1674tight positional0.060.05
1A1727medium positional0.090.5
2B1727medium positional0.110.5
3C1727medium positional0.090.5
4D1727medium positional0.080.5
1A1674tight thermal0.30.5
2B1674tight thermal0.330.5
3C1674tight thermal0.250.5
4D1674tight thermal0.230.5
1A1727medium thermal0.312
2B1727medium thermal0.322
3C1727medium thermal0.282
4D1727medium thermal0.242
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 458 -
Rwork0.188 8435 -
obs--95.96 %
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)
10.80010.04310.2770.3322-0.16470.2064-0.0095-0.02490.01580.003-0.008-0.0008-0.0302-0.00950.01750.08460.00740.0230.08730.01930.071710.638-32.484-5.204
20.4907-0.3575-0.21560.79610.29570.1622-0.01160.05070.01160.04910.0356-0.0166-0.0108-0.0366-0.0240.1058-0.01040.00160.0972-0.0210.09122.944-67.326-33.319
30.5849-0.0924-0.28330.6937-0.00280.23730.1299-0.0263-0.0535-0.1053-0.10690.08940.04090.0572-0.02310.13860.0396-0.07150.0713-0.04260.09052.971-24.387-54.52
40.7898-0.25350.27270.7029-0.42570.2910.08260.1687-0.06890.0447-0.02450.05950.02350.0241-0.05810.1370.0113-0.00440.12420.02140.057824.834-63.71616.252
50.17870.24930.28930.39620.48960.78810.01850.1822-0.03170.18450.3468-0.09030.14170.6302-0.36530.29590.26870.04260.6396-0.25990.251717.904-40.592-8.613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 543
2X-RAY DIFFRACTION2B79 - 545
3X-RAY DIFFRACTION3C79 - 544
4X-RAY DIFFRACTION4D79 - 545
5X-RAY DIFFRACTION5A2 - 7
6X-RAY DIFFRACTION5B5
7X-RAY DIFFRACTION5D1 - 3

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