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- PDB-4fva: Crystal structure of truncated Caenorhabditis elegans TDP2 -

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Basic information

Entry
Database: PDB / ID: 4fva
TitleCrystal structure of truncated Caenorhabditis elegans TDP2
Components5'-tyrosyl-DNA phosphodiesterase
KeywordsHYDROLASE / 5'-phosphotyrosyl-DNA diesterase
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 / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / : / UBA-like domain / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / UBA-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / 5'-tyrosyl-DNA phosphodiesterase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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
B: 5'-tyrosyl-DNA phosphodiesterase
C: 5'-tyrosyl-DNA phosphodiesterase
D: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,79730
Polymers117,1344
Non-polymers1,66326
Water10,160564
1
A: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6587
Polymers29,2831
Non-polymers3756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,88410
Polymers29,2831
Non-polymers6019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6587
Polymers29,2831
Non-polymers3756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 5'-tyrosyl-DNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5966
Polymers29,2831
Non-polymers3135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 104.400, 84.700
Angle α, β, γ (deg.)90.00, 90.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29283.492 Da / Num. of mol.: 4 / Fragment: unp residues 107-362
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 293 K / pH: 5
Details: 30% PEG 3,350 and 0.2M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 66104 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.16
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.566 / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1066)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→44.993 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 1672 3.03 %
Rwork0.1591 --
obs0.1606 55258 99.16 %
all-55259 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→44.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8063 0 107 564 8734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088329
X-RAY DIFFRACTIONf_angle_d1.10611186
X-RAY DIFFRACTIONf_dihedral_angle_d12.4413075
X-RAY DIFFRACTIONf_chiral_restr0.0721178
X-RAY DIFFRACTIONf_plane_restr0.0051448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.13090.26861410.2034422X-RAY DIFFRACTION98
2.1309-2.19970.25511350.18614432X-RAY DIFFRACTION99
2.1997-2.27830.25451400.18524447X-RAY DIFFRACTION99
2.2783-2.36950.24381320.1784414X-RAY DIFFRACTION99
2.3695-2.47740.21431420.17194449X-RAY DIFFRACTION99
2.4774-2.6080.24551420.16394450X-RAY DIFFRACTION99
2.608-2.77130.21171400.1634472X-RAY DIFFRACTION99
2.7713-2.98530.20011400.16024459X-RAY DIFFRACTION99
2.9853-3.28560.20841420.16114496X-RAY DIFFRACTION100
3.2856-3.76080.21471370.13974494X-RAY DIFFRACTION100
3.7608-4.73740.16571380.12814506X-RAY DIFFRACTION100
4.7374-45.00410.19651430.16694545X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 13.4368 Å / Origin y: 1.3072 Å / Origin z: -20.5082 Å
111213212223313233
T0.1984 Å2-0.019 Å20.0105 Å2-0.2168 Å20.0061 Å2--0.1954 Å2
L0.2064 °2-0.2221 °20.1189 °2-0.3223 °2-0.0555 °2--0.1608 °2
S-0.0149 Å °0.0086 Å °0.0019 Å °0.0191 Å °-0.0041 Å °-0.0043 Å °0.0011 Å °-0.0278 Å °0.0324 Å °
Refinement TLS groupSelection details: all

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