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

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Basic information

Entry
Database: PDB / ID: 8ysr
TitleCrystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with hexatungstotellurate(VI) TEW
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
6-tungstotellurate(VI) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9642
Polymers39,3491
Non-polymers1,6151
Water4,774265
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)35.367, 46.798, 60.374
Angle α, β, γ (deg.)100.48, 104.89, 100.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nucleotidyltransferase


Mass: 39349.109 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: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O24TeW6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.0, 16% w/v Polyethylene glycol 10,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1.21366 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: 1.21366 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. obs: 21801 / % possible obs: 96.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.636
Reflection shellResolution: 2.04→2.12 Å / Num. unique obs: 2159 / CC1/2: 0.983

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.04→25.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.468 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21548 1983 9.2 %RANDOM
Rwork0.18083 ---
obs0.18402 19654 95.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.573 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20.13 Å20.08 Å2
2---0.59 Å2-2.48 Å2
3---2.58 Å2
Refinement stepCycle: 1 / Resolution: 2.04→25.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 31 265 2950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132738
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172518
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.663703
X-RAY DIFFRACTIONr_angle_other_deg1.5531.5925798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36322.134164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91815466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3091522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7472.9421323
X-RAY DIFFRACTIONr_mcbond_other2.7482.9411322
X-RAY DIFFRACTIONr_mcangle_it4.0954.3991652
X-RAY DIFFRACTIONr_mcangle_other4.0944.41653
X-RAY DIFFRACTIONr_scbond_it3.8363.3611415
X-RAY DIFFRACTIONr_scbond_other3.5933.3321394
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8144.8242018
X-RAY DIFFRACTIONr_long_range_B_refined7.66435.2343163
X-RAY DIFFRACTIONr_long_range_B_other7.40234.1843073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.041→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 124 -
Rwork0.216 1246 -
obs--82.38 %

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