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

ID or keywords:

Entry

Database: PDB / ID: 8ysi

Title

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

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: 1.897 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	8ysi.cif.gz	90.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ysi.ent.gz	63.1 KB	Display	PDB format
PDBx/mmJSON format	8ysi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ysi_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	8ysi_full_validation.pdf.gz	1 MB	Display
Data in XML	8ysi_validation.xml.gz	19.2 KB	Display
Data in CIF	8ysi_validation.cif.gz	26.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/8ysi ftp://data.pdbj.org/pub/pdb/validation_reports/ys/8ysi	HTTPS FTP

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Related structure data

Related structure data	8yscC 8ysdC 8yseC 8ysgC 8ysjC 8yskC 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

40.2 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)	35.375, 46.302, 60.792
Angle α, β, γ (deg.)	101.796, 106.802, 95.768
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.: 2 / Source method: obtained synthetically / Formula: C₉H₁₅N₂O₁₅P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.34 Å³/Da / Density % sol: 47.54 %
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 05A / Wavelength: 0.99984 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 27, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99984 Å / Relative weight: 1
Reflection	Resolution: 1.897→30 Å / Num. obs: 26575 / % possible obs: 94.7 % / Redundancy: 2.4 % / R_merge(I) obs: 0.038 / Net I/σ(I): 21.865
Reflection shell	Resolution: 1.897→1.97 Å / Num. unique obs: 2733 / CC_1/2: 0.983

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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: 1.897→23.452 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.933 / SU B: 2.89 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.207	1320	4.978 %
R_work	0.1752	25197	-
all	0.177	-	-
obs	-	26517	93.975 %

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: 24.106 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.095 Å²	-0.015 Å²	0.146 Å²
2-	-	-0.18 Å²	-0.301 Å²
3-	-	-	0.125 Å²

Refinement step

Cycle: LAST / Resolution: 1.897→23.452 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2616	0	58	254	2928

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	2735
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2514
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	1.654	3708
X-RAY DIFFRACTION	r_angle_other_deg	1.308	1.593	5791
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.731	5	324
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.389	22.05	161
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.466	15	460
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.556	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	345
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3078
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	658
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	567
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	2292
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	1342
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1265
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.2	181
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.157	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.187	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	2.314	2.269	1302
X-RAY DIFFRACTION	r_mcbond_other	2.314	2.267	1301
X-RAY DIFFRACTION	r_mcangle_it	3.371	3.385	1624
X-RAY DIFFRACTION	r_mcangle_other	3.371	3.387	1625
X-RAY DIFFRACTION	r_scbond_it	3.137	2.696	1433
X-RAY DIFFRACTION	r_scbond_other	3.136	2.697	1434
X-RAY DIFFRACTION	r_scangle_it	4.859	3.917	2084
X-RAY DIFFRACTION	r_scangle_other	4.858	3.918	2085
X-RAY DIFFRACTION	r_lrange_it	6.547	26.83	3158
X-RAY DIFFRACTION	r_lrange_other	6.466	26.646	3115

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 (%)
1.897-1.946	0.221	89	0.196	1724	X-RAY DIFFRACTION	87.3735
1.946-1.999	0.228	86	0.181	1860	X-RAY DIFFRACTION	95.8621
1.999-2.057	0.209	82	0.177	1829	X-RAY DIFFRACTION	96.8576
2.057-2.12	0.234	94	0.173	1775	X-RAY DIFFRACTION	96.8896
2.12-2.189	0.2	105	0.158	1695	X-RAY DIFFRACTION	96.8784
2.189-2.265	0.215	101	0.174	1618	X-RAY DIFFRACTION	96.5188
2.265-2.35	0.213	86	0.163	1632	X-RAY DIFFRACTION	97.3371
2.35-2.446	0.196	80	0.154	1515	X-RAY DIFFRACTION	96.3164
2.446-2.554	0.206	69	0.161	1462	X-RAY DIFFRACTION	96.4106
2.554-2.677	0.214	82	0.167	1365	X-RAY DIFFRACTION	95.3856
2.677-2.821	0.198	68	0.174	1285	X-RAY DIFFRACTION	94.4832
2.821-2.991	0.195	66	0.176	1261	X-RAY DIFFRACTION	94.3141
2.991-3.195	0.235	68	0.167	1134	X-RAY DIFFRACTION	91.896
3.195-3.447	0.158	40	0.181	1041	X-RAY DIFFRACTION	90.3091
3.447-3.771	0.194	45	0.179	953	X-RAY DIFFRACTION	90.3167
3.771-4.208	0.19	44	0.177	854	X-RAY DIFFRACTION	89.1758
4.208-4.844	0.208	40	0.169	744	X-RAY DIFFRACTION	88.4876
4.844-5.894	0.25	23	0.208	675	X-RAY DIFFRACTION	90.4145
5.894-8.179	0.227	35	0.201	492	X-RAY DIFFRACTION	92.2942
8.179-23.452	0.184	17	0.197	283	X-RAY DIFFRACTION	84.9858

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