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- PDB-4f1i: Crystal structure of SeMet TDP2 from Caenorhabditis elegans -

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Basic information

Entry
Database: PDB / ID: 4f1i
TitleCrystal structure of SeMet TDP2 from Caenorhabditis elegans
Components5'-tyrosyl-DNA phosphodiesterase
KeywordsHYDROLASE / 5'-tyrosyl DNA phosphodiesterase
Function / homology
Function and homology information


5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / PML body / double-strand break repair / single-stranded DNA binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
: / : / UBA-like domain / UBA-like domain / Ubiquitin-associated (UBA) domain / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily ...: / : / UBA-like domain / UBA-like domain / Ubiquitin-associated (UBA) domain / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-tyrosyl-DNA phosphodiesterase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShi, K. / Kurahashi, K. / Aihara, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Authors: Shi, K. / Kurahashi, K. / Gao, R. / Tsutakawa, S.E. / Tainer, J.A. / Pommier, Y. / Aihara, H.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2439
Polymers41,5061
Non-polymers7378
Water2,558142
1
A: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules

A: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,48518
Polymers83,0122
Non-polymers1,47416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8360 Å2
ΔGint-31 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.685, 100.685, 121.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase


Mass: 41505.898 Da / Num. of mol.: 1 / Fragment: unp residues 21-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Y63D3A.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9XWG3, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 293 K / pH: 6
Details: PEG 6.000, 0.3M ammonium chloride, and 0.1M MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 9, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23342 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.828 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Iceicedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.185 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1134 5.11 %
Rwork0.1822 --
obs0.1845 22208 99.95 %
all-22208 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9055 Å20 Å2-0 Å2
2--2.9055 Å2-0 Å2
3----5.8111 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 48 142 2816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042720
X-RAY DIFFRACTIONf_angle_d0.8783652
X-RAY DIFFRACTIONf_dihedral_angle_d15.538999
X-RAY DIFFRACTIONf_chiral_restr0.074389
X-RAY DIFFRACTIONf_plane_restr0.002469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61390.32061250.25432586X-RAY DIFFRACTION100
2.6139-2.75170.28331680.22822559X-RAY DIFFRACTION100
2.7517-2.92410.26111540.20612574X-RAY DIFFRACTION100
2.9241-3.14980.28111570.20972579X-RAY DIFFRACTION100
3.1498-3.46670.26181300.1912644X-RAY DIFFRACTION100
3.4667-3.96810.20581280.16412630X-RAY DIFFRACTION100
3.9681-4.99840.16561280.14252677X-RAY DIFFRACTION100
4.9984-46.1930.23631440.19312825X-RAY DIFFRACTION100
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)
12.42110.1844-0.56422.2503-6.90022.1396-0.7250.77810.2501-0.5867-0.4641-0.8419-1.18691.03021.2580.6787-0.1844-0.0880.5306-0.05440.528731.233975.789276.4529
22.12672.07656.27761.95732.0882.0562-0.09260.61260.72960.20440.5224-0.677-1.2210.2087-0.36940.67310.1401-0.08340.5171-0.05530.624334.932275.192892.5234
36.9477-0.7319-2.82750.3452-0.00941.46750.06421.83250.48760.5336-0.5451-0.99941.1793-0.8244-0.0441.1828-0.3535-0.11420.9158-0.00461.084446.210977.193186.6136
42.06095.6923-2.52345.35930.14511.16920.4863-1.39611.0240.5893-0.3289-0.6626-1.62280.94230.01180.8327-0.3431-0.07571.4622-0.21941.008156.593466.739985.1138
52.0579-4.0180.11072.02795.42161.208-0.1734-0.33310.07761.911-0.3917-1.63770.97491.12760.35440.77370.1404-0.10681.2433-0.18410.957750.767458.629386.4667
62.71172.37095.41997.30525.55085.8598-0.82641.458-0.3808-0.91091.7606-1.907-0.43962.7095-0.87470.738-0.1158-0.01771.4052-0.31470.881553.858258.308976.0165
70.3765-1.0524-0.86327.95654.69642.5018-0.3189-0.22580.02860.9003-0.03760.22231.0946-0.46190.41860.81090.1989-0.08481.0036-0.25010.577244.453138.408777.4859
82.8306-1.0421-7.09932.6068-0.19182.2847-0.0445-0.5019-0.40360.7052-0.0872-0.04720.75340.8310.17240.4979-0.05860.00430.49630.04050.449653.906320.789764.512
95.7434-1.1196-3.61726.72511.53146.9319-0.02270.4352-0.3556-0.4218-0.138-0.28080.6635-0.0450.17250.3578-0.00080.00550.283-0.03180.292857.092613.865144.344
104.89480.311-1.03936.3167-0.71472.9218-0.23440.7341-0.3968-0.72790.01370.22620.7835-0.86250.27980.3729-0.06730.0270.4585-0.07460.354847.644215.399844.0249
112.8668-6.13372.36972.6422-8.05212.4774-0.4798-1.04820.01041.17040.81730.3309-0.9122-1.3626-0.72520.5748-0.01150.00990.7855-0.07290.678740.535522.879654.8256
127.44111.4666-4.43948.9794-3.52664.3692-0.08110.94490.2514-0.87680.22920.15080.1149-0.2966-0.15750.36860.0211-0.02150.55390.04410.304148.901131.277339.5225
136.59632.4915-7.17735.0441-2.73492.91310.15030.03720.3196-0.00020.16440.3819-0.1054-0.392-0.32910.20870.00360.00050.42930.02750.259148.228127.757952.7362
143.1658-8.1317-1.63049.7565.42856.98870.304-0.10290.2347-0.5346-0.2617-0.1179-0.92860.4947-0.0480.42880.00150.07680.36320.0650.409858.691137.939641.211
153.2912-0.3014-1.69083.7652-1.06966.17310.3580.05490.40760.5428-0.26830.1555-0.7218-0.5275-0.08940.3734-0.00070.02960.2915-0.03030.328352.11334.609953.3863
162.18573.2019-3.1532.14610.39692.16882.1380.36072.2215-1.0016-0.3718-0.2733-3.3604-0.1212-1.60730.9697-0.10440.18140.63120.10580.60163.26541.168948.8979
172.3735-6.336-0.97789.3331-1.67142.34530.0036-0.90141.36091.02360.2064-0.5325-1.09990.5002-0.31120.5427-0.04740.07710.4894-0.05920.533260.055735.184658.4235
186.0966-1.8531-4.50627.94014.30942.9657-0.0346-0.60890.26920.14510.1701-0.34920.03771.0135-0.32540.3437-0.03640.00920.3840.00840.342771.22223.331448.6547
195.1819-2.8219-5.09914.0321.8647.68570.38570.5180.0036-0.2494-0.4251-0.3695-0.2046-0.41680.28960.3535-0.0226-0.00370.36610.00910.339266.189928.089947.6259
206.4369-4.623-5.47886.75455.47664.4253-0.2361-0.3828-0.18160.24040.3193-0.05260.70450.4539-0.01780.34590.01170.02230.29490.03060.309764.322816.97852.2645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 21:27)
2X-RAY DIFFRACTION2(chain A and resid 28:34)
3X-RAY DIFFRACTION3(chain A and resid 35:41)
4X-RAY DIFFRACTION4(chain A and resid 42:52)
5X-RAY DIFFRACTION5(chain A and resid 53:61)
6X-RAY DIFFRACTION6(chain A and resid 62:89)
7X-RAY DIFFRACTION7(chain A and resid 90:114)
8X-RAY DIFFRACTION8(chain A and resid 115:123)
9X-RAY DIFFRACTION9(chain A and resid 124:161)
10X-RAY DIFFRACTION10(chain A and resid 162:193)
11X-RAY DIFFRACTION11(chain A and resid 194:201)
12X-RAY DIFFRACTION12(chain A and resid 202:217)
13X-RAY DIFFRACTION13(chain A and resid 218:235)
14X-RAY DIFFRACTION14(chain A and resid 236:251)
15X-RAY DIFFRACTION15(chain A and resid 252:276)
16X-RAY DIFFRACTION16(chain A and resid 277:281)
17X-RAY DIFFRACTION17(chain A and resid 282:290)
18X-RAY DIFFRACTION18(chain A and resid 291:311)
19X-RAY DIFFRACTION19(chain A and resid 312:329)
20X-RAY DIFFRACTION20(chain A and resid 330:362)

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