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- PDB-9f7j: Rhodococcus diDNase in apo state -

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Basic information

Entry
Database: PDB / ID: 9f7j
TitleRhodococcus diDNase in apo state
ComponentsdiDNase
KeywordsHYDROLASE / DNase DEDDy family Dinuclease
Biological speciesRhodococcus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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

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Assembly

Deposited unit
A: diDNase


Theoretical massNumber of molelcules
Total (without water)23,6991
Polymers23,6991
Non-polymers00
Water3,549197
1
A: diDNase

A: diDNase


Theoretical massNumber of molelcules
Total (without water)47,3992
Polymers47,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area2410 Å2
ΔGint-26 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.745, 60.353, 134.514
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-422-

HOH

21A-483-

HOH

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Components

#1: Protein diDNase


Mass: 23699.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus ruber (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% PEG3350, 0.1 M sodium acetate pH 4.5, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.72→39.28 Å / Num. obs: 22757 / % possible obs: 99.78 % / Redundancy: 13.3 % / Biso Wilson estimate: 22.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.0498 / Net I/σ(I): 11.13
Reflection shellResolution: 1.72→1.781 Å / Rmerge(I) obs: 2.034 / Num. unique obs: 2228 / CC1/2: 0.774 / Rpim(I) all: 0.5617

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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: 1.72→39.28 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 1939 8.56 %
Rwork0.1778 39448 -
obs0.1805 22751 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.32 Å2
Refinement stepCycle: LAST / Resolution: 1.72→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 0 197 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631602
X-RAY DIFFRACTIONf_angle_d0.87312188
X-RAY DIFFRACTIONf_chiral_restr0.0558264
X-RAY DIFFRACTIONf_plane_restr0.0105279
X-RAY DIFFRACTIONf_dihedral_angle_d5.582216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.3241390.29311486X-RAY DIFFRACTION99.69
1.74-1.770.29121390.27351496X-RAY DIFFRACTION99.94
1.77-1.790.31081470.28711555X-RAY DIFFRACTION99.88
1.79-1.820.28911470.25411537X-RAY DIFFRACTION99.7
1.82-1.850.29161360.23931503X-RAY DIFFRACTION99.88
1.85-1.880.24661400.23371518X-RAY DIFFRACTION99.88
1.88-1.910.25321380.22961509X-RAY DIFFRACTION99.76
1.91-1.940.26651420.2181505X-RAY DIFFRACTION99.88
1.94-1.980.27971500.20741560X-RAY DIFFRACTION99.94
1.98-2.020.24541390.19761473X-RAY DIFFRACTION100
2.02-2.070.2181460.17891544X-RAY DIFFRACTION100
2.07-2.110.18931390.18821499X-RAY DIFFRACTION99.88
2.11-2.170.20741420.16861511X-RAY DIFFRACTION99.04
2.17-2.230.19291450.1681540X-RAY DIFFRACTION99.94
2.23-2.290.19411400.15521501X-RAY DIFFRACTION100
2.29-2.360.2271460.16421524X-RAY DIFFRACTION99.82
2.37-2.450.1991400.16771521X-RAY DIFFRACTION100
2.45-2.550.1961450.17191498X-RAY DIFFRACTION100
2.55-2.660.24281400.17411535X-RAY DIFFRACTION100
2.66-2.80.19771400.17511519X-RAY DIFFRACTION100
2.8-2.980.20611440.17381527X-RAY DIFFRACTION100
2.98-3.210.20451400.17041522X-RAY DIFFRACTION100
3.21-3.530.1751370.16591515X-RAY DIFFRACTION100
3.53-4.040.16461440.15061505X-RAY DIFFRACTION98.86
4.04-5.090.19541410.15331524X-RAY DIFFRACTION99.82
5.09-39.280.21321450.18311521X-RAY DIFFRACTION99.7

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