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- PDB-9f7d: Rhodococcus diDNase bound to deoxy-pGG -

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Basic information

Entry
Database: PDB / ID: 9f7d
TitleRhodococcus diDNase bound to deoxy-pGG
Components
  • DNA (5'-D(P*GP*G)-3')
  • diDNase
KeywordsHYDROLASE / DNase DEDDy family Dinuclease
Function / homologyDNA
Function and homology information
Biological speciesRhodococcus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: diDNase
D: DNA (5'-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3483
Polymers24,3132
Non-polymers351
Water2,540141
1
A: diDNase
D: DNA (5'-D(P*GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)48,6976
Polymers48,6264
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area4860 Å2
ΔGint-53 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.837, 61.298, 135.109
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-494-

HOH

21A-527-

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: DNA chain DNA (5'-D(P*GP*G)-3')


Mass: 613.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rhodococcus ruber (bacteria)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 44.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium chloride, 20%(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: 2→39.58 Å / Num. obs: 14916 / % possible obs: 99.76 % / Redundancy: 13.2 % / Biso Wilson estimate: 32.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.04542 / Net I/σ(I): 14
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 1.389 / Num. unique obs: 1457 / CC1/2: 0.865 / Rpim(I) all: 0.3926

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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: 2→39.58 Å / SU ML: 0.2085 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 1406 10.03 %
Rwork0.1834 25236 -
obs0.1879 14902 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.72 Å2
Refinement stepCycle: LAST / Resolution: 2→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 45 1 141 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731698
X-RAY DIFFRACTIONf_angle_d1.04252328
X-RAY DIFFRACTIONf_chiral_restr0.0642280
X-RAY DIFFRACTIONf_plane_restr0.0129289
X-RAY DIFFRACTIONf_dihedral_angle_d7.0913241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.31681400.27591257X-RAY DIFFRACTION99.93
2.03-2.070.29361390.26391257X-RAY DIFFRACTION99.43
2.07-2.110.34681420.25891274X-RAY DIFFRACTION99.93
2.11-2.150.24821390.25371259X-RAY DIFFRACTION99.86
2.15-2.20.26241420.23521251X-RAY DIFFRACTION99.93
2.2-2.250.30191390.26681259X-RAY DIFFRACTION99.79
2.25-2.310.32361390.22761238X-RAY DIFFRACTION100
2.31-2.370.26531490.21681311X-RAY DIFFRACTION99.86
2.37-2.440.21651330.19061218X-RAY DIFFRACTION100
2.44-2.520.20761500.20881298X-RAY DIFFRACTION100
2.52-2.610.23831370.20141243X-RAY DIFFRACTION100
2.61-2.710.27041420.20491280X-RAY DIFFRACTION99.86
2.71-2.840.2711370.19851260X-RAY DIFFRACTION100
2.84-2.990.29041360.20461241X-RAY DIFFRACTION99.78
2.99-3.170.20371440.19371284X-RAY DIFFRACTION99.58
3.17-3.420.251440.18711247X-RAY DIFFRACTION99.86
3.42-3.760.21541420.1571255X-RAY DIFFRACTION100
3.76-4.310.20151420.14061271X-RAY DIFFRACTION99.93
4.31-5.410.18521400.14291254X-RAY DIFFRACTION99.86
5.43-39.580.17121360.15151279X-RAY DIFFRACTION99.37
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.598520427690.403616028682-1.137805073124.05117225671-0.6028307019264.02333724678-0.0827438253514-0.0357546291782-0.03674147367960.03576596227420.008539922818120.05274824559010.1951383607830.02692739141990.06541882235840.197108549290.0131826937525-0.02096416852410.2381527982380.004708453726530.22344403781617.42573004014.4747649419-12.6195281484
22.58800031599-0.520768865787-1.556057998730.9654569016920.5484790123043.453516372070.00895075384870.125244873130.0804458583102-0.00205665862546-0.0609007693980.0963856844472-0.214365734621-0.1635569564910.05574612718770.2123352600890.0221037369637-0.03281325129090.205129825155-0.005125703519170.21422780461213.230998691711.3879129782-24.5775349681
32.60102330220.6080403730351.600306573496.662299641523.92419410772.92735147236-0.4439782813820.2100325591830.6962276182040.1638258372960.01519514936380.0103739003466-1.287108932550.04939545316470.4290108761950.466606647139-0.0215712725383-0.04794021787490.4256425325320.01389074773290.40801946469814.575080286219.8032822284-18.0029636244
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 101 )AA8 - 1011 - 94
22chain 'A' and (resid 102 through 213 )AA102 - 21395 - 206
33chain 'D' and (resid 603 through 604 )DB603 - 604

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