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- PDB-9f7g: Nocardioides diDNase bound to deoxy-pGG -

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Basic information

Entry
Database: PDB / ID: 9f7g
TitleNocardioides diDNase bound to deoxy-pGG
Components
  • DNA (5'-D(P*GP*G)-3')
  • Ribonuclease D
KeywordsHYDROLASE / DNase DEDDy family Dinuclease
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding
Similarity search - Function
: / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / Ribonuclease D
Similarity search - Component
Biological speciesNocardioides sp. S-1144 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMortensen, S. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01GM123609 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria.
Authors: Mortensen, S. / Kuncova, S. / Lormand, J.D. / Myers, T.M. / Kim, S.K. / Lee, V.T. / Winkler, W.C. / Sondermann, H.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease D
C: DNA (5'-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5323
Polymers23,4362
Non-polymers961
Water5,152286
1
A: Ribonuclease D
C: DNA (5'-D(P*GP*G)-3')
hetero molecules

A: Ribonuclease D
C: DNA (5'-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0656
Polymers46,8724
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4830 Å2
ΔGint-48 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.030, 85.221, 149.056
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
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

21A-598-

HOH

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Components

#1: Protein Ribonuclease D


Mass: 22822.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardioides sp. S-1144 (bacteria) / Gene: FE634_02320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B7RB63
#2: DNA chain DNA (5'-D(P*GP*G)-3')


Mass: 613.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nocardioides sp. S-1144 (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M bis-tris (pH 5.5), 25%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.55→40.97 Å / Num. obs: 32636 / % possible obs: 98.93 % / Redundancy: 11.5 % / Biso Wilson estimate: 14.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07467 / Rpim(I) all: 0.02225 / Net I/σ(I): 22.03
Reflection shellResolution: 1.55→1.605 Å / Rmerge(I) obs: 0.3845 / Num. unique obs: 2974 / CC1/2: 0.931 / Rpim(I) all: 0.1819

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→40.97 Å / SU ML: 0.1222 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.5554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.18 1908 5.82 %
Rwork0.1435 58013 -
obs0.1456 32633 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.63 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 45 5 286 1924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051706
X-RAY DIFFRACTIONf_angle_d0.74632340
X-RAY DIFFRACTIONf_chiral_restr0.0526266
X-RAY DIFFRACTIONf_plane_restr0.0045296
X-RAY DIFFRACTIONf_dihedral_angle_d13.382622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.21531070.17721806X-RAY DIFFRACTION79.31
1.57-1.590.19131230.1462090X-RAY DIFFRACTION89.85
1.59-1.610.18011280.13352089X-RAY DIFFRACTION95.03
1.61-1.640.16471390.13042227X-RAY DIFFRACTION97.13
1.64-1.660.18671410.12312221X-RAY DIFFRACTION98.66
1.66-1.690.16531380.13152257X-RAY DIFFRACTION99.63
1.69-1.720.16541400.12342276X-RAY DIFFRACTION99.96
1.72-1.750.16371400.11912281X-RAY DIFFRACTION99.92
1.75-1.790.16561410.11922238X-RAY DIFFRACTION100
1.79-1.820.15181370.12052275X-RAY DIFFRACTION99.92
1.82-1.860.19971460.12262245X-RAY DIFFRACTION100
1.86-1.910.15621370.12882272X-RAY DIFFRACTION100
1.91-1.950.19591410.12212284X-RAY DIFFRACTION99.96
1.95-2.010.20121360.13462247X-RAY DIFFRACTION99.92
2.01-2.060.16231430.13122291X-RAY DIFFRACTION99.96
2.06-2.130.18591370.1362241X-RAY DIFFRACTION100
2.13-2.210.16751400.12962306X-RAY DIFFRACTION100
2.21-2.30.18071440.13972247X-RAY DIFFRACTION100
2.3-2.40.16691410.13442257X-RAY DIFFRACTION99.96
2.4-2.530.15941360.15812271X-RAY DIFFRACTION99.96
2.53-2.690.19591440.16132288X-RAY DIFFRACTION100
2.69-2.890.2121400.16112252X-RAY DIFFRACTION99.92
2.89-3.180.20021400.15252266X-RAY DIFFRACTION99.92
3.18-3.640.1851420.14852242X-RAY DIFFRACTION100
3.64-4.590.18231380.1422287X-RAY DIFFRACTION100
4.59-40.970.16341450.1652257X-RAY DIFFRACTION99.75

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