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- PDB-6k1d: Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP -

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Basic information

Entry
Database: PDB / ID: 6k1d
TitleCrystal structure of EXD2 exonuclease domain soaked in Mn and GMP
ComponentsExonuclease 3'-5' domain-containing protein 2
KeywordsHYDROLASE / 3'-5' exonuclease / DnaQ family
Function / homology
Function and homology information


exodeoxyribonuclease I / DNA double-strand break processing / nucleic acid metabolic process / 3'-5'-DNA exonuclease activity / 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 / DNA double-strand break processing / nucleic acid metabolic process / 3'-5'-DNA exonuclease activity / 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 / mitochondrial outer membrane / nucleic acid binding / 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: 3 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 / _struct_conn.ptnr2_label_seq_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)49,0126
Polymers48,7922
Non-polymers2204
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-81 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.528, 73.931, 132.543
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, 2-(N-morpholino)ethanesulfonic acid, Calcium acetate, Dithiothreitol, Manganese Chloride, Guanosine monophosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97936 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9290 / % possible obs: 95.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 465

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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: 3→49.348 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.13
RfactorNum. reflection% reflection
Rfree0.2771 462 4.98 %
Rwork0.2121 --
obs0.2153 9270 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→49.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 4 18 3002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013020
X-RAY DIFFRACTIONf_angle_d1.3694094
X-RAY DIFFRACTIONf_dihedral_angle_d14.8761120
X-RAY DIFFRACTIONf_chiral_restr0.051499
X-RAY DIFFRACTIONf_plane_restr0.008513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9967-3.43020.3341520.25292913X-RAY DIFFRACTION97
3.4302-4.32130.28351500.21312836X-RAY DIFFRACTION93
4.3213-49.35420.25181600.19663059X-RAY DIFFRACTION96
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)
11.4275-0.16662.00010.1904-0.63135.9965-0.10750.15330.1197-0.1166-0.17-0.1116-0.0460.44680.31480.33580.0360.00910.30330.05190.43796.3333-3.621428.9537
21.2486-0.15521.36280.2124-1.11165.9756-0.1254-0.01840.07420.0552-0.10.08180.1606-0.04450.10690.3290.01620.01870.1996-0.00740.3564-6.7865-3.152315.8981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 77 through 294)
2X-RAY DIFFRACTION2(chain 'B' and resid 77 through 292)

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