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

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Basic information

Entry
Database: PDB / ID: 8ysu
TitleCrystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with CTP
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
CYTIDINE-5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 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)40,2335
Polymers39,2181
Non-polymers1,0154
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-31 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.363, 111.506, 46.981
Angle α, β, γ (deg.)90.000, 100.415, 90.000
Int Tables number4
Space group name H-MP1211

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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-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / 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.: 244 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS propane pH 9.0, 30% w/v Polyethylene glycol 6,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 25742 / % possible obs: 98.2 % / Redundancy: 6.5 % / CC1/2: 0.995 / Net I/σ(I): 15.424
Reflection shellResolution: 1.94→2.01 Å / Num. unique obs: 2511 / CC1/2: 0.705

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.944→23.881 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.742 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2389 1245 5.188 %
Rwork0.2021 23867 -
all0.204 --
obs-25173 95.635 %
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: 26.792 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20.269 Å2
2---0.032 Å20 Å2
3----0.053 Å2
Refinement stepCycle: LAST / Resolution: 1.944→23.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 60 244 2951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132768
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172534
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.6543754
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5935837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03422.134164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94115464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6821522
X-RAY DIFFRACTIONr_chiral_restr0.0650.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
X-RAY DIFFRACTIONr_nbd_refined0.220.2605
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.22387
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21341
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2185
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.212
X-RAY DIFFRACTIONr_nbd_other0.2570.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.210
X-RAY DIFFRACTIONr_mcbond_it2.2072.6041319
X-RAY DIFFRACTIONr_mcbond_other2.1932.6031318
X-RAY DIFFRACTIONr_mcangle_it3.4123.8931647
X-RAY DIFFRACTIONr_mcangle_other3.4133.8951648
X-RAY DIFFRACTIONr_scbond_it3.0243.0581449
X-RAY DIFFRACTIONr_scbond_other2.8872.9441438
X-RAY DIFFRACTIONr_scangle_it4.9094.5172107
X-RAY DIFFRACTIONr_scangle_other4.9084.5242108
X-RAY DIFFRACTIONr_lrange_it8.35631.1543210
X-RAY DIFFRACTIONr_lrange_other8.33531.0373167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.944-1.9940.33800.3021444X-RAY DIFFRACTION78.3145
1.994-2.0490.294850.2621603X-RAY DIFFRACTION89.1236
2.049-2.1080.287910.2381592X-RAY DIFFRACTION93.552
2.108-2.1720.3141050.2351634X-RAY DIFFRACTION97.4776
2.172-2.2430.257920.2181615X-RAY DIFFRACTION97.7663
2.243-2.3210.266890.2111525X-RAY DIFFRACTION97.8182
2.321-2.4090.238800.2041502X-RAY DIFFRACTION98.4443
2.409-2.5060.293740.1971423X-RAY DIFFRACTION96.2701
2.506-2.6170.248810.1921360X-RAY DIFFRACTION96.5818
2.617-2.7430.216870.1711328X-RAY DIFFRACTION98.4006
2.743-2.8910.219630.1851268X-RAY DIFFRACTION99.0327
2.891-3.0640.223620.2061207X-RAY DIFFRACTION99.2181
3.064-3.2730.249520.2121156X-RAY DIFFRACTION99.0976
3.273-3.5320.215590.2081077X-RAY DIFFRACTION99.214
3.532-3.8640.226430.184975X-RAY DIFFRACTION98.7391
3.864-4.3110.215480.169872X-RAY DIFFRACTION98.3957
4.311-4.9610.223350.181780X-RAY DIFFRACTION97.3716
4.961-6.0340.2350.224670X-RAY DIFFRACTION99.1561
6.034-8.3660.217290.194521X-RAY DIFFRACTION99.278
8.366-23.8810.161160.166313X-RAY DIFFRACTION96.4809

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