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

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Basic information

Entry
Database: PDB / ID: 8ysg
TitleCrystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with GTP
ComponentsNucleotidyltransferase
KeywordsTRANSFERASE / CD-NTase
Function / homology
Function and homology information


nucleotide metabolic process / nucleotidyltransferase activity / defense response to virus / GTP binding / 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
GUANOSINE-5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.171 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

Downloads & links

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Assembly

Deposited unit
A: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3135
Polymers39,2181
Non-polymers1,0954
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.033, 100.404, 46.398
Angle α, β, γ (deg.)90.000, 101.621, 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#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.: 111 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate, 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: 2.17→30 Å / Num. obs: 16522 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 47.211
Reflection shellResolution: 2.17→2.25 Å / Num. unique obs: 1572 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.171→22.734 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.834 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.253
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2718 824 4.995 %
Rwork0.2417 15674 -
all0.243 --
obs-16498 99.356 %
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: 37.635 Å2
Baniso -1Baniso -2Baniso -3
1--0.014 Å2-0 Å2-0.022 Å2
2---0.079 Å2-0 Å2
3---0.093 Å2
Refinement stepCycle: LAST / Resolution: 2.171→22.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 66 111 2762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132712
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172424
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.6543678
X-RAY DIFFRACTIONr_angle_other_deg1.2441.595628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1265318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29922.037162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55915457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4751522
X-RAY DIFFRACTIONr_chiral_restr0.060.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.220.2649
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22453
X-RAY DIFFRACTIONr_nbtor_refined0.170.21262
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1680.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2230.218
X-RAY DIFFRACTIONr_nbd_other0.2370.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.26
X-RAY DIFFRACTIONr_mcbond_it3.3493.9041278
X-RAY DIFFRACTIONr_mcbond_other3.3413.9031277
X-RAY DIFFRACTIONr_mcangle_it5.255.8481594
X-RAY DIFFRACTIONr_mcangle_other5.2495.8491595
X-RAY DIFFRACTIONr_scbond_it2.9644.2071434
X-RAY DIFFRACTIONr_scbond_other2.964.2041432
X-RAY DIFFRACTIONr_scangle_it4.7026.2272084
X-RAY DIFFRACTIONr_scangle_other4.7016.2312085
X-RAY DIFFRACTIONr_lrange_it8.98245.0613134
X-RAY DIFFRACTIONr_lrange_other8.98245.0453127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.171-2.2270.351490.321108X-RAY DIFFRACTION97.0638
2.227-2.2880.35620.3181132X-RAY DIFFRACTION100
2.288-2.3540.463710.3141107X-RAY DIFFRACTION100
2.354-2.4260.337420.3071058X-RAY DIFFRACTION100
2.426-2.5050.343590.3051039X-RAY DIFFRACTION100
2.505-2.5920.315530.312988X-RAY DIFFRACTION100
2.592-2.6890.31480.292984X-RAY DIFFRACTION100
2.689-2.7980.282520.264916X-RAY DIFFRACTION100
2.798-2.9210.272390.263921X-RAY DIFFRACTION100
2.921-3.0630.286490.255831X-RAY DIFFRACTION99.8865
3.063-3.2260.371400.261824X-RAY DIFFRACTION99.8844
3.226-3.420.228410.248763X-RAY DIFFRACTION100
3.42-3.6520.272370.235720X-RAY DIFFRACTION100
3.652-3.940.228440.214682X-RAY DIFFRACTION100
3.94-4.3090.191290.189624X-RAY DIFFRACTION100
4.309-4.8050.172280.166565X-RAY DIFFRACTION100
4.805-5.5250.253290.181492X-RAY DIFFRACTION100
5.525-6.710.262210.194437X-RAY DIFFRACTION99.7821
6.71-9.260.181200.176333X-RAY DIFFRACTION98.3287
9.26-22.7340.225110.201150X-RAY DIFFRACTION74.1936

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