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

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Basic information

Entry
Database: PDB / ID: 8yse
TitleCrystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with dATP
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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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)40,2495
Polymers39,2181
Non-polymers1,0314
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.355, 46.614, 59.644
Angle α, β, γ (deg.)99.56, 105.81, 100.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nucleotidyltransferase


Mass: 39217.918 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-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 147 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2 % v/v Tacsimate, 0.1 M Bis-Tris pH 6.5, 20 % 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: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.19→30 Å / Num. obs: 17231 / % possible obs: 96.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 37.853
Reflection shellResolution: 2.19→2.28 Å / Redundancy: 2.2 % / Num. unique obs: 1695 / CC1/2: 0.995 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.502 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19571 853 5.1 %RANDOM
Rwork0.16353 ---
obs0.16521 16353 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0.03 Å20.1 Å2
2--0.06 Å2-0.54 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.19→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 62 147 2836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0142751
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172380
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.6943729
X-RAY DIFFRACTIONr_angle_other_deg0.9621.6575595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84922.037162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68115462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3481522
X-RAY DIFFRACTIONr_chiral_restr0.0680.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
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_it3.1043.2981306
X-RAY DIFFRACTIONr_mcbond_other3.1033.2971305
X-RAY DIFFRACTIONr_mcangle_it4.644.931629
X-RAY DIFFRACTIONr_mcangle_other4.6394.9321630
X-RAY DIFFRACTIONr_scbond_it3.7953.6991445
X-RAY DIFFRACTIONr_scbond_other3.7943.71446
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9265.42101
X-RAY DIFFRACTIONr_long_range_B_refined7.53437.7133126
X-RAY DIFFRACTIONr_long_range_B_other7.54237.6693113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 55 -
Rwork0.176 1087 -
obs--85.61 %

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