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- PDB-8zef: Crystal structure of Staphylococcus aureus DinG protein in comple... -

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Basic information

Entry
Database: PDB / ID: 8zef
TitleCrystal structure of Staphylococcus aureus DinG protein in complex with ssDNA and Ca2+
Components
  • 3'-5' exonuclease DinG
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*TP*T)-3')
KeywordsHYDROLASE/DNA / exonuclease / DNA repair / 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)
chemical production metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsCheng, K. / Gao, T. / Hao, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
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
DepositionMay 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,8125
Polymers107,7323
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-57 kcal/mol
Surface area42350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.855, 128.045, 302.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: 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
#2: 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.) chemical production metagenome (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2084.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) chemical production metagenome (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 5% v/v Tacsimate (pH 7.0), 0.1 M HEPES (pH 7.0), 8% w/v Polyethylene glycol monomethyl ether 5,000 and 50 mM CaCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.21→39.65 Å / Num. obs: 22275 / % possible obs: 99.58 % / Redundancy: 6 % / Biso Wilson estimate: 111.43 Å2 / Rmerge(I) obs: 0.102 / Net I/av σ(I): 17.3 / Net I/σ(I): 2.43
Reflection shellResolution: 3.21→3.33 Å / Rmerge(I) obs: 1.514 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3207

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→39.65 Å / SU ML: 0.5115 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.3298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2917 1106 4.97 %
Rwork0.2833 21169 -
obs0.2836 22275 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 154.64 Å2
Refinement stepCycle: LAST / Resolution: 3.21→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 216 2 0 7498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817657
X-RAY DIFFRACTIONf_angle_d1.154810369
X-RAY DIFFRACTIONf_chiral_restr0.0871169
X-RAY DIFFRACTIONf_plane_restr0.01241282
X-RAY DIFFRACTIONf_dihedral_angle_d11.73521054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.360.4731410.42112602X-RAY DIFFRACTION99.6
3.36-3.540.39221240.37252612X-RAY DIFFRACTION99.49
3.54-3.760.35931330.34682600X-RAY DIFFRACTION99.49
3.76-4.050.3441430.34162656X-RAY DIFFRACTION99.61
4.05-4.450.33061260.29262598X-RAY DIFFRACTION99.53
4.45-5.10.30681530.26682651X-RAY DIFFRACTION99.93
5.1-6.420.29851410.30742668X-RAY DIFFRACTION99.82
6.42-39.650.21611450.22552782X-RAY DIFFRACTION99.22
Refinement TLS params.Method: refined / Origin x: 43.4539309831 Å / Origin y: -5.58812741543 Å / Origin z: 38.4348454159 Å
111213212223313233
T0.898517691439 Å2-0.0811774448144 Å2-0.13157171614 Å2-1.1241300014 Å20.186632786639 Å2--0.901358283128 Å2
L1.41359412621 °2-0.112041866488 °2-0.087657207426 °2-1.06207496819 °20.0412183502652 °2--1.53843827346 °2
S-0.0387384474461 Å °-0.711900959895 Å °-0.0509431013664 Å °0.503933377744 Å °-0.00384941880686 Å °-0.309157628481 Å °-0.184739558248 Å °0.263049271444 Å °0.0728031498405 Å °
Refinement TLS groupSelection details: all

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