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- PDB-9qrf: Ancestral protein of diDNase -

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Basic information

Entry
Database: PDB / ID: 9qrf
TitleAncestral protein of diDNase
Componentsancestor of diDNase
KeywordsDE NOVO PROTEIN / Ancestor / dinuclease / diDNase / NrnC
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMortensen, S. / Burnim, A. / Dufault-Thompson, K. / Jiang, X. / Lipka, A.E. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 AI142400 United States
CitationJournal: Sci Adv / Year: 2026
Title: Ancestral proteins trace the emergence of substrate specificity and oligomerization within bacterial DEDDy dinucleases.
Authors: Mortensen, S. / Burnim, A.A. / Dufault-Thompson, K. / Lipka, A.E. / Jiang, X. / Sondermann, H.
History
DepositionApr 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ancestor of diDNase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1652
Polymers24,1301
Non-polymers351
Water2,738152
1
A: ancestor of diDNase
hetero molecules

A: ancestor of diDNase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3304
Polymers48,2592
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2800 Å2
ΔGint-39 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.903, 70.948, 48.241
Angle α, β, γ (deg.)90.000, 115.807, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

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Components

#1: Protein ancestor of diDNase


Mass: 24129.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES (pH 5), 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.45→47.45 Å / Num. obs: 36862 / % possible obs: 96.65 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06764 / Net I/σ(I): 14.42
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.7653 / Num. unique obs: 25793 / CC1/2: 0.976 / % possible all: 95.28

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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: 1.45→47.45 Å / SU ML: 0.1519 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2004 3132 4.36 %
Rwork0.1659 68743 -
obs0.1674 36840 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.36 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 1 152 1783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581680
X-RAY DIFFRACTIONf_angle_d0.90852281
X-RAY DIFFRACTIONf_chiral_restr0.0849262
X-RAY DIFFRACTIONf_plane_restr0.0101298
X-RAY DIFFRACTIONf_dihedral_angle_d5.2342228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.33361400.25053091X-RAY DIFFRACTION93.52
1.47-1.50.27121390.22163016X-RAY DIFFRACTION93.48
1.5-1.520.22261390.19313116X-RAY DIFFRACTION95.34
1.52-1.550.22371390.16963073X-RAY DIFFRACTION95
1.55-1.580.18931450.16793198X-RAY DIFFRACTION96.87
1.58-1.610.25551440.15823130X-RAY DIFFRACTION95.15
1.61-1.650.19881410.15653140X-RAY DIFFRACTION96.73
1.65-1.690.18541370.15043106X-RAY DIFFRACTION96.12
1.69-1.730.19621450.15983155X-RAY DIFFRACTION95.38
1.73-1.770.22411390.15862981X-RAY DIFFRACTION92.88
1.77-1.830.22531450.16013178X-RAY DIFFRACTION97.51
1.83-1.890.17621450.15033169X-RAY DIFFRACTION97.13
1.89-1.950.22071460.15293162X-RAY DIFFRACTION96.84
1.95-2.030.19771470.14863221X-RAY DIFFRACTION97.48
2.03-2.120.17111390.16333105X-RAY DIFFRACTION96.98
2.12-2.240.21171460.14873198X-RAY DIFFRACTION96.93
2.24-2.380.15511390.16473118X-RAY DIFFRACTION95.15
2.38-2.560.20881380.15992990X-RAY DIFFRACTION92.24
2.56-2.820.21631440.19143196X-RAY DIFFRACTION97.58
2.82-3.220.20831450.18343175X-RAY DIFFRACTION97.22
3.22-4.060.20021460.16513125X-RAY DIFFRACTION95.84
4.06-47.450.18551440.15763100X-RAY DIFFRACTION94.94

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