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- PDB-9ii8: Crystal structure of Staphylococcus aureus DinG protein in comple... -

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Basic information

Entry
Database: PDB / ID: 9ii8
TitleCrystal structure of Staphylococcus aureus DinG protein in complex with ssDNA
Components
  • 3'-5' exonuclease DinG
  • DNA (5'-D(P*TP*TP*TP*T)-3')
KeywordsHYDROLASE/DNA / helicase / nuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA replication proofreading / 3'-5' exonuclease activity / helicase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / DNA binding / ATP binding / cytosol
Similarity search - Function
3'-5' exonuclease DinG / DNA polymerase III epsilon subunit, exonuclease domain / Exonuclease / HELICc2 / ATP-dependent helicase, C-terminal / Exonuclease, RNase T/DNA polymerase III / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / EXOIII ...3'-5' exonuclease DinG / DNA polymerase III epsilon subunit, exonuclease domain / Exonuclease / HELICc2 / ATP-dependent helicase, C-terminal / Exonuclease, RNase T/DNA polymerase III / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / EXOIII / Superfamilies 1 and 2 helicase C-terminal domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / 3'-5' exonuclease DinG
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsCheng, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270043 China
CitationJournal: To Be Published
Title: Structure of Staphylococcus aureus DinG
Authors: Cheng, K. / Gao, T. / Hao, W.
History
DepositionJun 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(P*TP*TP*TP*T)-3')
A: 3'-5' exonuclease DinG


Theoretical massNumber of molelcules
Total (without water)105,6472
Polymers105,6472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-6 kcal/mol
Surface area41710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.170, 229.170, 128.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: DNA chain DNA (5'-D(P*TP*TP*TP*T)-3')


Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Protein 3'-5' exonuclease DinG


Mass: 104475.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Gene: dinG, SAOUHSC_01472 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FYH5, Hydrolases; Acting on ester bonds
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: 3.99 Å3/Da / Density % sol: 69.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M LiSO4, 0.1 M MES (pH 6.5), and 15% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97936 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 3.16→111.77 Å / Num. obs: 29417 / % possible obs: 99.95 % / Redundancy: 8 % / Biso Wilson estimate: 115.64 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 3.4
Reflection shellResolution: 3.16→3.273 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 2913 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.16→111.77 Å / SU ML: 0.5623 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.293 1478 5.02 %
Rwork0.2687 27939 -
obs0.2699 29417 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119.65 Å2
Refinement stepCycle: LAST / Resolution: 3.16→111.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7352 80 0 0 7432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01137582
X-RAY DIFFRACTIONf_angle_d1.376210242
X-RAY DIFFRACTIONf_chiral_restr0.09681153
X-RAY DIFFRACTIONf_plane_restr0.01891290
X-RAY DIFFRACTIONf_dihedral_angle_d7.12061000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.260.49061410.50442490X-RAY DIFFRACTION100
3.26-3.380.461220.39832524X-RAY DIFFRACTION100
3.38-3.510.34371400.32742488X-RAY DIFFRACTION100
3.51-3.670.33081380.29452501X-RAY DIFFRACTION100
3.67-3.870.32761270.30782545X-RAY DIFFRACTION99.96
3.87-4.110.30651190.29892505X-RAY DIFFRACTION100
4.11-4.430.27751300.25462533X-RAY DIFFRACTION100
4.43-4.870.26741480.23712517X-RAY DIFFRACTION99.96
4.87-5.580.25751480.25132553X-RAY DIFFRACTION100
5.58-7.030.30721280.29592581X-RAY DIFFRACTION100
7.03-111.770.26061370.22392702X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: 5.86308597258 Å / Origin y: 52.9556964717 Å / Origin z: 31.4544964426 Å
111213212223313233
T0.664777645483 Å2-0.11155299355 Å20.074823334506 Å2-0.74737970334 Å2-0.0590778709053 Å2--0.586231251681 Å2
L0.897111263931 °20.363333717919 °20.0171460994621 °2-1.29722546 °2-0.420967729634 °2--0.309383887361 °2
S-0.0933945867278 Å °0.345503088028 Å °-0.263354024583 Å °-0.375607564948 Å °0.0982395304446 Å °-0.0250662657282 Å °0.0415789989298 Å °0.0968496983927 Å °-0.00418778686157 Å °
Refinement TLS groupSelection details: all

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