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- PDB-6k19: Crystal structure of EXD2 exonuclease domain soaked in Mg -

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Basic information

Entry
Database: PDB / ID: 6k19
TitleCrystal structure of EXD2 exonuclease domain soaked in Mg
ComponentsExonuclease 3'-5' domain-containing protein 2
KeywordsHYDROLASE / 3'-5' exonuclease / DnaQ family
Function / homology
Function and homology information


exodeoxyribonuclease I / nucleic acid metabolic process / 3'-5'-DNA exonuclease activity / DNA double-strand break processing / single-stranded DNA 3'-5' DNA exonuclease activity / intermediate filament cytoskeleton / replication fork processing / site of DNA damage / 3'-5' exonuclease activity / double-strand break repair via homologous recombination ...exodeoxyribonuclease I / nucleic acid metabolic process / 3'-5'-DNA exonuclease activity / DNA double-strand break processing / single-stranded DNA 3'-5' DNA exonuclease activity / intermediate filament cytoskeleton / replication fork processing / site of DNA damage / 3'-5' exonuclease activity / double-strand break repair via homologous recombination / double-strand break repair / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial outer membrane / mitochondrial matrix / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus / cytoplasm
Similarity search - Function
: / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Exonuclease 3'-5' domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsPark, J. / Lee, C.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination.
Authors: Park, J. / Lee, S.Y. / Jeong, H. / Kang, M.G. / Van Haute, L. / Minczuk, M. / Seo, J.K. / Jun, Y. / Myung, K. / Rhee, H.W. / Lee, C.
History
DepositionMay 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exonuclease 3'-5' domain-containing protein 2
B: Exonuclease 3'-5' domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8414
Polymers48,7922
Non-polymers492
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-70 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.347, 74.107, 133.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exonuclease 3'-5' domain-containing protein 2 / Exonuclease 3'-5' domain-like-containing protein 2


Mass: 24396.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXD2, C14orf114, EXDL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVH0, exodeoxyribonuclease I
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, 2-(N-morpholino)ethanesulfonic acid, Calcium acetate, Dithiothreitol, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23379 / % possible obs: 98.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.35
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.359 / Num. unique obs: 1108

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K17

6k17


Resolution: 2.202→39.295 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.07
RfactorNum. reflection% reflection
Rfree0.2515 1166 5 %
Rwork0.1992 --
obs0.2019 23307 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.202→39.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 2 180 3183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073073
X-RAY DIFFRACTIONf_angle_d1.074165
X-RAY DIFFRACTIONf_dihedral_angle_d13.8441139
X-RAY DIFFRACTIONf_chiral_restr0.039504
X-RAY DIFFRACTIONf_plane_restr0.004522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2019-2.30210.26921280.23972431X-RAY DIFFRACTION88
2.3021-2.42350.3421440.23872709X-RAY DIFFRACTION96
2.4235-2.57530.33841450.23152757X-RAY DIFFRACTION97
2.5753-2.77410.28581430.21422719X-RAY DIFFRACTION97
2.7741-3.05320.27921470.21462808X-RAY DIFFRACTION99
3.0532-3.49470.26871500.19192823X-RAY DIFFRACTION99
3.4947-4.40210.22091510.17522885X-RAY DIFFRACTION100
4.4021-39.30120.21161580.19173009X-RAY DIFFRACTION99
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)
11.14050.37922.5840.15731.12317.5032-0.1512-0.11610.07890.0219-0.06020.0868-0.1003-0.48260.19780.19860.04350.00990.2574-0.03240.320317.136533.6718103.4346
20.63020.19251.65520.06850.72166.6068-0.17750.010.0036-0.0285-0.08250.01910.0386-0.05760.16130.22660.0140.03080.21910.01330.33829.410334.2075117.5356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 77:293 )A77 - 293
2X-RAY DIFFRACTION2( CHAIN B AND RESID 77:293 )B77 - 293

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