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- PDB-9ouf: Crystal structure of an ADP-ribosyl hydrolase from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 9ouf
TitleCrystal structure of an ADP-ribosyl hydrolase from Streptococcus parasanguinis
ComponentsRibonuclease
KeywordsHYDROLASE / ADP-ribosyl Cyclase/hydrolase / toxin / antibacterial
Function / homology: / LXG domain / LXG domain profile. / Hydrolases; Acting on ester bonds / hydrolase activity / Ribonuclease
Function and homology information
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsColautti, J. / Kim, Y. / Whitney, J.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173486 Canada
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Antibacterial ADP-ribosyl cyclase toxins inhibit bacterial growth by rapidly depleting NAD(P).
Authors: Colautti, J. / Kim, Y. / Whitney, J.C.
History
DepositionMay 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9715
Polymers17,8031
Non-polymers1684
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.185, 59.151, 40.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Ribonuclease


Mass: 17802.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Gene: SPLFYP13_01488 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A6N3DPK9, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.9 Å3/Da / Density % sol: 35.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M BisTrisHCl pH 5.5, 17 % PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2025
RadiationMonochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.39→33.18 Å / Num. obs: 28170 / % possible obs: 99.4 % / Redundancy: 11.2 % / Biso Wilson estimate: 14.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.052 / Rrim(I) all: 0.129 / Net I/σ(I): 9.7
Reflection shellResolution: 1.39→1.46 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.271 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3879 / CC1/2: 0.576 / Rpim(I) all: 0.64 / Rrim(I) all: 1.429 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→33.18 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.0413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1973 1378 4.9 %
Rwork0.1698 26731 -
obs0.1713 28109 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.45 Å2
Refinement stepCycle: LAST / Resolution: 1.39→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 7 96 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931232
X-RAY DIFFRACTIONf_angle_d0.94261676
X-RAY DIFFRACTIONf_chiral_restr0.0946186
X-RAY DIFFRACTIONf_plane_restr0.0084222
X-RAY DIFFRACTIONf_dihedral_angle_d12.1911462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.430.34531250.3212469X-RAY DIFFRACTION93.54
1.44-1.490.30311520.25312631X-RAY DIFFRACTION99.93
1.49-1.560.24151480.1942634X-RAY DIFFRACTION99.75
1.56-1.640.22581510.16622636X-RAY DIFFRACTION99.96
1.64-1.750.22411440.16452672X-RAY DIFFRACTION99.93
1.75-1.880.2015940.15332696X-RAY DIFFRACTION99.89
1.88-2.070.17611140.13912697X-RAY DIFFRACTION100
2.07-2.370.19081310.15112732X-RAY DIFFRACTION100
2.37-2.980.18511340.17092735X-RAY DIFFRACTION99.97
2.98-33.180.17631850.16492829X-RAY DIFFRACTION100

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