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

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Basic information

Entry
Database: PDB / ID: 8ysn
TitleCrystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB Ear-cut mutant
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
PHOSPHATE ION / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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

Downloads & links

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Assembly

Deposited unit
A: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3472
Polymers37,2521
Non-polymers951
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-5 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.344, 73.161, 101.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleotidyltransferase


Mass: 37251.785 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M Sodium fluoride, 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 07A / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.01→30 Å / Num. obs: 25160 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.996 / Net I/σ(I): 27.311
Reflection shellResolution: 2.01→2.08 Å / Num. unique obs: 2467 / CC1/2: 0.904

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→22.206 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.75 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2082 1254 5.021 %
Rwork0.1785 23837 -
all0.18 --
obs-25097 99.635 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.104 Å2
Baniso -1Baniso -2Baniso -3
1-0.021 Å2-0 Å20 Å2
2--0.655 Å20 Å2
3----0.676 Å2
Refinement stepCycle: LAST / Resolution: 2.01→22.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 5 199 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132561
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172378
X-RAY DIFFRACTIONr_angle_refined_deg1.461.6453458
X-RAY DIFFRACTIONr_angle_other_deg1.3931.5925478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4922.171152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04915435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2561520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
X-RAY DIFFRACTIONr_nbd_refined0.20.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22143
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21268
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2151
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.213
X-RAY DIFFRACTIONr_nbd_other0.2480.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.212
X-RAY DIFFRACTIONr_mcbond_it2.9632.8721259
X-RAY DIFFRACTIONr_mcbond_other2.9512.8691258
X-RAY DIFFRACTIONr_mcangle_it4.4344.2941572
X-RAY DIFFRACTIONr_mcangle_other4.4344.2981573
X-RAY DIFFRACTIONr_scbond_it3.6473.1871302
X-RAY DIFFRACTIONr_scbond_other3.613.1891299
X-RAY DIFFRACTIONr_scangle_it5.6844.6181886
X-RAY DIFFRACTIONr_scangle_other5.6224.6191881
X-RAY DIFFRACTIONr_lrange_it7.39732.9342936
X-RAY DIFFRACTIONr_lrange_other7.33332.7382900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.0620.2751000.2431686X-RAY DIFFRACTION97.0125
2.062-2.1180.3900.2141664X-RAY DIFFRACTION100
2.118-2.180.284680.1941671X-RAY DIFFRACTION100
2.18-2.2460.248610.1951623X-RAY DIFFRACTION100
2.246-2.320.249890.1931541X-RAY DIFFRACTION99.9387
2.32-2.40.205860.1751486X-RAY DIFFRACTION100
2.4-2.490.195780.1721465X-RAY DIFFRACTION100
2.49-2.5910.199770.1711386X-RAY DIFFRACTION100
2.591-2.7060.204820.1811331X-RAY DIFFRACTION99.9293
2.706-2.8370.272650.1941295X-RAY DIFFRACTION100
2.837-2.9890.195730.1751230X-RAY DIFFRACTION100
2.989-3.1680.231590.1921163X-RAY DIFFRACTION100
3.168-3.3840.203660.1871102X-RAY DIFFRACTION100
3.384-3.6510.253630.1951024X-RAY DIFFRACTION100
3.651-3.9940.207490.17949X-RAY DIFFRACTION100
3.994-4.4550.146500.135877X-RAY DIFFRACTION100
4.455-5.1260.147380.142789X-RAY DIFFRACTION100
5.126-6.2320.188240.187678X-RAY DIFFRACTION100
6.232-8.630.132250.161544X-RAY DIFFRACTION100
8.63-22.2060.141170.17333X-RAY DIFFRACTION95.1087

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