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

ID or keywords:

Entry

Database: PDB / ID: 8ysk

Title

Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with UTP Mn

Components

Nucleotidyltransferase

Keywords

TRANSFERASE / 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

Biological species

Deinococcus wulumuqiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.984 Å

Authors

Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.

Funding support

Taiwan, 1items

Citation

Journal: 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

Deposition	Mar 23, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ysk.cif.gz	89.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8ysk.ent.gz	62.4 KB	Display	PDB format
PDBx/mmJSON format	8ysk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ysk_validation.pdf.gz	759.1 KB	Display	wwPDB validaton report
Full document	8ysk_full_validation.pdf.gz	760.4 KB	Display
Data in XML	8ysk_validation.xml.gz	18 KB	Display
Data in CIF	8ysk_validation.cif.gz	24.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/8ysk ftp://data.pdbj.org/pub/pdb/validation_reports/ys/8ysk	HTTPS FTP

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Related structure data

Related structure data	8yscC 8ysdC 8yseC 8ysgC 8ysiC 8ysjC 8yslC 8ysmC 8ysnC 8ysoC 8ysqC 8ysrC 8yssC 8ysuC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nucleotidyltransferase

hetero molecules

39.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	35.274, 46.091, 59.889
Angle α, β, γ (deg.)	101.137, 106.903, 95.429
Int Tables number	1
Space group name H-M	P1

#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-UTP / URIDINE 5'-TRIPHOSPHATE Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₅N₂O₁₅P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.53 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M MOPS pH 6.5, 20% w/v Polyethylene glycol 4,000.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 20, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97626 Å / Relative weight: 1
Reflection	Resolution: 1.984→30 Å / Num. obs: 23181 / % possible obs: 96.4 % / Redundancy: 6.6 % / CC_1/2: 0.997 / Net I/σ(I): 25
Reflection shell	Resolution: 1.984→2.06 Å / Num. unique obs: 2212 / CC_1/2: 0.965

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Blu-Ice		data collection
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.984→23.245 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.94 / SU B: 3.869 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2092	1092	4.937 %
R_work	0.1667	21025	-
all	0.169	-	-
obs	-	22117	91.404 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.829 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.034 Å²	-0.262 Å²	0.263 Å²
2-	-	-0.418 Å²	-0.683 Å²
3-	-	-	0.481 Å²

Refinement step

Cycle: LAST / Resolution: 1.984→23.245 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2647	0	31	194	2872

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2738
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2522
X-RAY DIFFRACTION	r_angle_refined_deg	1.352	1.651	3707
X-RAY DIFFRACTION	r_angle_other_deg	1.291	1.593	5810
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.738	5	329
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.805	22.134	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.019	15	464
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.098	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	342
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3118
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	662
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	533
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	2289
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	1342
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1261
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	155
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.144	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.416	2.923	1319
X-RAY DIFFRACTION	r_mcbond_other	2.415	2.922	1318
X-RAY DIFFRACTION	r_mcangle_it	3.505	4.371	1647
X-RAY DIFFRACTION	r_mcangle_other	3.504	4.373	1648
X-RAY DIFFRACTION	r_scbond_it	3.053	3.287	1419
X-RAY DIFFRACTION	r_scbond_other	3.052	3.288	1420
X-RAY DIFFRACTION	r_scangle_it	4.739	4.784	2060
X-RAY DIFFRACTION	r_scangle_other	4.737	4.784	2061
X-RAY DIFFRACTION	r_lrange_it	6.116	33.215	3099
X-RAY DIFFRACTION	r_lrange_other	6.074	33.095	3072

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.984-2.036	0.261	72	0.181	1106	X-RAY DIFFRACTION	66.8559
2.036-2.091	0.238	58	0.181	1320	X-RAY DIFFRACTION	77.9853
2.091-2.152	0.211	68	0.182	1341	X-RAY DIFFRACTION	83.969
2.152-2.217	0.208	75	0.181	1402	X-RAY DIFFRACTION	88.4431
2.217-2.29	0.281	72	0.186	1380	X-RAY DIFFRACTION	93.3762
2.29-2.37	0.22	67	0.166	1427	X-RAY DIFFRACTION	96.0772
2.37-2.458	0.247	73	0.184	1298	X-RAY DIFFRACTION	94.617
2.458-2.558	0.214	63	0.173	1323	X-RAY DIFFRACTION	94.7368
2.558-2.671	0.209	64	0.165	1193	X-RAY DIFFRACTION	92.1554
2.671-2.8	0.223	63	0.166	1219	X-RAY DIFFRACTION	98.7673
2.8-2.95	0.229	56	0.166	1191	X-RAY DIFFRACTION	98.4992
2.95-3.127	0.265	64	0.17	1112	X-RAY DIFFRACTION	98.9899
3.127-3.341	0.216	48	0.163	1039	X-RAY DIFFRACTION	98.7284
3.341-3.605	0.178	52	0.161	960	X-RAY DIFFRACTION	98.1571
3.605-3.943	0.209	35	0.153	912	X-RAY DIFFRACTION	97.9317
3.943-4.399	0.172	39	0.144	793	X-RAY DIFFRACTION	96.8568
4.399-5.061	0.136	37	0.147	697	X-RAY DIFFRACTION	93.9821
5.061-6.155	0.234	41	0.197	578	X-RAY DIFFRACTION	99.3579
6.155-8.527	0.206	31	0.178	473	X-RAY DIFFRACTION	98.8235
8.527-23.245	0.15	14	0.162	261	X-RAY DIFFRACTION	92.5926

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