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- PDB-8yss: Crystal structure of the apo form of Deinococcus wulumuqiensis CD... -

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Basic information

Entry
Database: PDB / ID: 8yss
TitleCrystal structure of the apo form of Deinococcus wulumuqiensis CD-NTase DwCdnB
ComponentsNucleotidyltransferase
KeywordsTRANSFERASE / CD-NTase
Function / homology: / Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / nucleotide metabolic process / nucleotidyltransferase activity / defense response to virus / ATP binding / metal ion binding / Cyclic GMP-AMP synthase
Function and homology information
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 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 23, 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


Theoretical massNumber of molelcules
Total (without water)39,4991
Polymers39,4991
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.344, 111.153, 47.120
Angle α, β, γ (deg.)90.00, 100.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleotidyltransferase


Mass: 39499.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus wulumuqiensis (bacteria) / Gene: DVJ83_15700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A345ILN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.7, 10 % v/v 2-Propanol, 16 % w/v Polyethylene glycol 4,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97857 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: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 30856 / % possible obs: 97.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 33.225
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 3004 / CC1/2: 0.946

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.83→26.77 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.1963 3926 6.48 %
Rwork0.1642 --
obs0.1663 30824 97.39 %
Refinement stepCycle: LAST / Resolution: 1.83→26.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 0 394 3048

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