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- PDB-8ken: Structure of DexA reveal the novel mechanism of DNA catalysis -

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Basic information

Entry
Database: PDB / ID: 8ken
TitleStructure of DexA reveal the novel mechanism of DNA catalysis
ComponentsExodeoxyribonuclease
KeywordsDNA BINDING PROTEIN / DNA binding / DNA cut
Function / homology3'-5' exoribonuclease Rv2179c-like domain / 3'-5' exoribonuclease Rv2179c-like domain / exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / Ribonuclease H-like superfamily / Exodeoxyribonuclease
Function and homology information
Biological speciesEscherichia phage EcSzw_1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsLiu, Y.H. / Ma, B. / Kang, Y. / Liu, B. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China Postdoctoral Science Foundation2020M682420 China
CitationJournal: To Be Published
Title: The crystal structure of M-EXOD
Authors: Liu, Y.H.
History
DepositionAug 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Exodeoxyribonuclease
A: Exodeoxyribonuclease


Theoretical massNumber of molelcules
Total (without water)51,8712
Polymers51,8712
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-5 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.330, 82.182, 115.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Exodeoxyribonuclease


Mass: 25935.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage EcSzw_1 (virus) / Gene: dexA
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S (others)
References: UniProt: P04536
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.5 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 289 K / Method: evaporation, recrystallization
Details: 0.02M Magnesium Chloride, 0.1M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.38→67.05 Å / Num. obs: 29905 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.17 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.1
Reflection shellResolution: 2.38→7.53 Å / Rmerge(I) obs: 0.968 / Num. unique obs: 4290

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→67.05 Å / SU ML: 0.3532 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2844 1467 4.92 %
Rwork0.2402 28338 -
obs0.2424 29805 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.04 Å2
Refinement stepCycle: LAST / Resolution: 2.38→67.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 95 3481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753466
X-RAY DIFFRACTIONf_angle_d0.89484714
X-RAY DIFFRACTIONf_chiral_restr0.0602530
X-RAY DIFFRACTIONf_plane_restr0.008612
X-RAY DIFFRACTIONf_dihedral_angle_d5.8958470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.470.37041280.31572792X-RAY DIFFRACTION99.86
2.47-2.570.34421510.2782806X-RAY DIFFRACTION99.83
2.57-2.680.29281470.26882773X-RAY DIFFRACTION99.69
2.68-2.820.29341440.25882813X-RAY DIFFRACTION99.76
2.82-30.32921240.25312805X-RAY DIFFRACTION99.8
3-3.230.29751880.25322784X-RAY DIFFRACTION99.63
3.23-3.560.31541460.23442820X-RAY DIFFRACTION99.83
3.56-4.070.25051600.22622833X-RAY DIFFRACTION99.87
4.07-5.130.25931500.21412886X-RAY DIFFRACTION99.9
5.13-7.530.28151290.24273026X-RAY DIFFRACTION99.4

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