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- PDB-4fzy: Exonuclease X in complex with 12bp blunt-ended dsDNA -

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Basic information

Entry
Database: PDB / ID: 4fzy
TitleExonuclease X in complex with 12bp blunt-ended dsDNA
Components
  • DNA (5'-D(*TP*GP*TP*AP*GP*AP*TP*TP*CP*GP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*CP*GP*AP*AP*TP*CP*TP*AP*CP*A)-3')
  • Exodeoxyribonuclease 10
KeywordsHydrolase/DNA / Exo / DnaQ family / DEDDh / Exonuclease / Nuclease / Mismatch repair / UV repair / homologous recombination / stabilization of tandem repeat / Hydrolase-DNA complex
Function / homology
Function and homology information


DNA replication proofreading / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mismatch repair / 3'-5' exonuclease activity / nucleic acid binding / cytosol
Similarity search - Function
Exodeoxyribonuclease X-like, C-terminal / Exodeoxyribonuclease X-like C-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Exodeoxyribonuclease 10
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, T. / Sun, H. / Cheng, F. / Bi, L. / Jiang, T.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease
Authors: Wang, T. / Sun, H.L. / Cheng, F. / Zhang, X.E. / Bi, L. / Jiang, T.
History
DepositionJul 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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 / _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_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
C: DNA (5'-D(*TP*GP*TP*AP*GP*AP*TP*TP*CP*GP*AP*G)-3')
A: Exodeoxyribonuclease 10
D: DNA (5'-D(P*CP*TP*CP*GP*AP*AP*TP*CP*TP*AP*CP*A)-3')
B: Exodeoxyribonuclease 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5468
Polymers47,4544
Non-polymers924
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-68 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.282, 78.887, 146.668
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: DNA chain DNA (5'-D(*TP*GP*TP*AP*GP*AP*TP*TP*CP*GP*AP*G)-3')


Mass: 3717.439 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Exodeoxyribonuclease 10 / Exodeoxyribonuclease X / Exo X / Exonuclease X


Mass: 20065.205 Da / Num. of mol.: 2 / Fragment: UNP residues 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: exoX / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEK0, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters
#3: DNA chain DNA (5'-D(P*CP*TP*CP*GP*AP*AP*TP*CP*TP*AP*CP*A)-3')


Mass: 3606.381 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1M MES, 17% PEG6000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15314 / % possible obs: 99.8 %
Reflection shellResolution: 2.5→2.59 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FZX

4fzx


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / ESU R: 0.71 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24076 768 5 %RANDOM
Rwork0.21918 ---
all0.22025 14545 --
obs0.22023 14545 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.068 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2---2.46 Å20 Å2
3---4.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 472 4 22 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213245
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8422.1374510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95122.87115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.43815459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1031521
X-RAY DIFFRACTIONr_chiral_restr0.060.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212285
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_it1.2021.51665
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22822710
X-RAY DIFFRACTIONr_scbond_it3.38131580
X-RAY DIFFRACTIONr_scangle_it5.1864.51800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.497→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 58 -
Rwork0.3 1009 -
obs--97 %

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