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- PDB-8kel: Structure of DexA reveal the novel Mechanism of DNA catalysis -

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Basic information

Entry
Database: PDB / ID: 8kel
TitleStructure of DexA reveal the novel Mechanism of DNA catalysis
ComponentsExodeoxyribonuclease
KeywordsDNA BINDING PROTEIN / chlorinase / SAM / ClDA / FDA / ANTIBIOTIC / OXIDOREDUCTASE
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 coli 0.1197 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsLiu, Y.H. / Ma, B. / Kang, Y. / Liu, B. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172299 China
CitationJournal: To Be Published
Title: Structure of EXOD at 2.4 Angstroms resolution
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

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Assembly

Deposited unit
A: Exodeoxyribonuclease
B: Exodeoxyribonuclease
C: Exodeoxyribonuclease
D: Exodeoxyribonuclease


Theoretical massNumber of molelcules
Total (without water)103,9834
Polymers103,9834
Non-polymers00
Water00
1
A: Exodeoxyribonuclease
B: Exodeoxyribonuclease


Theoretical massNumber of molelcules
Total (without water)51,9912
Polymers51,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Exodeoxyribonuclease
D: Exodeoxyribonuclease


Theoretical massNumber of molelcules
Total (without water)51,9912
Polymers51,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.548, 76.285, 108.009
Angle α, β, γ (deg.)90.000, 93.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.951793382292, -0.278576918468, -0.128391035209), (-0.278492320202, -0.960250938354, 0.0189779603472), (-0.128574433748, 0.0176928202207, -0.991542020844)9.74156165566, 19.3261864035, 106.647569463
2given(0.981567799158, -0.176777388239, -0.0726251379569), (0.173818952974, 0.983736805375, -0.0452644378976), (0.0794457503153, 0.031806489248, 0.996331631536)44.6700384362, 19.9665920243, 54.1579481284

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Components

#1: Protein
Exodeoxyribonuclease


Mass: 25995.654 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 0.1197 (bacteria) / Gene: dexA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P04536
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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.02M Calcium chloride dihydrate, 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: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.88→35.94 Å / Num. obs: 30240 / % possible obs: 95.96 % / Redundancy: 4 % / Biso Wilson estimate: 70.54 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.25
Reflection shellResolution: 2.88→2.98 Å / Num. unique obs: 3066 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→35.94 Å / SU ML: 0.4335 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.2548
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2762 1434 4.77 %
Rwork0.2225 28622 -
obs0.225 30056 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.85 Å2
Refinement stepCycle: LAST / Resolution: 2.88→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 0 0 6550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00896694
X-RAY DIFFRACTIONf_angle_d1.0829089
X-RAY DIFFRACTIONf_chiral_restr0.05841017
X-RAY DIFFRACTIONf_plane_restr0.00981186
X-RAY DIFFRACTIONf_dihedral_angle_d7.2162891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.980.37371530.29362913X-RAY DIFFRACTION99.16
2.98-3.10.35331550.2662942X-RAY DIFFRACTION99.65
3.1-3.240.38321750.2512929X-RAY DIFFRACTION99.65
3.24-3.420.31051400.23462959X-RAY DIFFRACTION99.61
3.42-3.630.26751150.22872929X-RAY DIFFRACTION97.72
3.63-3.910.2888990.23272166X-RAY DIFFRACTION72.55
3.91-4.30.26851550.20932921X-RAY DIFFRACTION98.84
4.3-4.920.24991360.19672931X-RAY DIFFRACTION97.43
4.92-6.20.29511420.24982956X-RAY DIFFRACTION98.73
6.2-35.940.2241640.19642976X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 20.1862326079 Å / Origin y: -1.2054905967 Å / Origin z: 27.4364867559 Å
111213212223313233
T0.436484056932 Å20.00673395690591 Å2-0.0334192892096 Å2-0.424626455137 Å20.0812569866822 Å2--0.583848421435 Å2
L1.0399000338 °2-0.407801180355 °2-1.42475055925 °2-0.73111742144 °20.804994313991 °2--2.73027672255 °2
S0.0143200064421 Å °0.1441208628 Å °0.142534477372 Å °-0.149855031297 Å °0.0390703105085 Å °-0.0765506234968 Å °-0.00960094792165 Å °-0.132486436774 Å °-0.0497581455539 Å °
Refinement TLS groupSelection details: all

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