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- PDB-8ysd: Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdn... -

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Basic information

Entry
Database: PDB / ID: 8ysd
TitleCrystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with ATP (form 2)
ComponentsNucleotidyltransferase
KeywordsTRANSFERASE / CD-NTase
Function / homology
Function and homology information


nucleotide metabolic process / nucleotidyltransferase activity / defense response to virus / ATP binding / metal ion binding
Similarity search - Function
: / Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsWang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-039-001-MY3 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural insights into signaling promiscuity of the CBASS anti-phage defense system from a radiation-resistant bacterium.
Authors: Yang, C.S. / Shie, M.Y. / Huang, S.W. / Wang, Y.C. / Hou, M.H. / Chen, C.J. / Chen, Y.
History
DepositionMar 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4125
Polymers39,3491
Non-polymers1,0634
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.387, 46.809, 59.976
Angle α, β, γ (deg.)99.96, 105.81, 99.54
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Nucleotidyltransferase / DwCdnB


Mass: 39349.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first residue must be annotated as Met0 / Source: (gene. exp.) Deinococcus wulumuqiensis (bacteria) / Gene: DVJ83_15700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A345ILN6
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 6.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.61→30 Å / Num. obs: 44348 / % possible obs: 96.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 11.54 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 22.146
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 4.4 % / Num. unique obs: 4353 / CC1/2: 0.984 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→28.08 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2139 1980 4.52 %
Rwork0.1878 --
obs0.189 43824 95.13 %
Refinement stepCycle: LAST / Resolution: 1.61→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 64 358 3076

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