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

ID or keywords:

Entry

Database: PDB / ID: 8ysm

Title

Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with CTP 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: 1.5 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	8ysm.cif.gz	95 KB	Display	PDBx/mmCIF format
PDB format	pdb8ysm.ent.gz	66.3 KB	Display	PDB format
PDBx/mmJSON format	8ysm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ysm_validation.pdf.gz	821.9 KB	Display	wwPDB validaton report
Full document	8ysm_full_validation.pdf.gz	825.6 KB	Display
Data in XML	8ysm_validation.xml.gz	20.9 KB	Display
Data in CIF	8ysm_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/8ysm ftp://data.pdbj.org/pub/pdb/validation_reports/ys/8ysm	HTTPS FTP

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Related structure data

Related structure data	8yscC 8ysdC 8yseC 8ysgC 8ysiC 8ysjC 8yskC 8yslC 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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: Nucleotidyltransferase

hetero molecules

39.9 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)	35.401, 46.765, 64.182
Angle α, β, γ (deg.)	105.450, 103.349, 99.327
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-CTP / CYTIDINE-5'-TRIPHOSPHATE Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.47 Å³/Da / Density % sol: 50.15 %
Crystal grow	Temperature: 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

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: 1.5→30 Å / Num. obs: 57942 / % possible obs: 96.7 % / Redundancy: 6.8 % / CC_1/2: 1 / R_merge(I) obs: 0.044 / Net I/σ(I): 40.4
Reflection shell	Resolution: 1.5→1.55 Å / Num. unique obs: 5722 / CC_1/2: 0.978

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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: 1.5→23.508 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.955 / SU B: 1.154 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1927	2791	4.842 %
R_work	0.1734	54845	-
all	0.174	-	-
obs	-	57636	96.001 %

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: 19.78 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.015 Å²	-0.033 Å²	0.042 Å²
2-	-	-0.021 Å²	-0.152 Å²
3-	-	-	0.102 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→23.508 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2647	0	36	378	3061

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	2742
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2523
X-RAY DIFFRACTION	r_angle_refined_deg	1.445	1.651	3713
X-RAY DIFFRACTION	r_angle_other_deg	1.408	1.593	5811
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.528	5	329
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.48	22.134	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.074	15	464
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.974	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	342
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3120
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	663
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	539
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	2350
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	1356
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1298
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	216
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.185	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.29	0.2	30
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.171	0.2	28
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.041	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.142	1.837	1319
X-RAY DIFFRACTION	r_mcbond_other	2.142	1.835	1318
X-RAY DIFFRACTION	r_mcangle_it	3.211	2.752	1647
X-RAY DIFFRACTION	r_mcangle_other	3.21	2.755	1648
X-RAY DIFFRACTION	r_scbond_it	2.88	2.138	1423
X-RAY DIFFRACTION	r_scbond_other	2.864	2.143	1408
X-RAY DIFFRACTION	r_scangle_it	4.453	3.083	2066
X-RAY DIFFRACTION	r_scangle_other	4.432	3.082	2061
X-RAY DIFFRACTION	r_lrange_it	5.975	21.93	3193
X-RAY DIFFRACTION	r_lrange_other	5.799	21.398	3103

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 (%)
1.5-1.539	0.248	199	0.225	3742	X-RAY DIFFRACTION	88.4823
1.539-1.581	0.246	193	0.209	3902	X-RAY DIFFRACTION	95.2769
1.581-1.627	0.22	174	0.19	3884	X-RAY DIFFRACTION	96.619
1.627-1.677	0.211	210	0.18	3754	X-RAY DIFFRACTION	96.4712
1.677-1.732	0.216	173	0.184	3583	X-RAY DIFFRACTION	95.6699
1.732-1.792	0.215	186	0.183	3471	X-RAY DIFFRACTION	95.4083
1.792-1.86	0.209	178	0.176	3458	X-RAY DIFFRACTION	97.3233
1.86-1.935	0.183	204	0.177	3202	X-RAY DIFFRACTION	97.7893
1.935-2.021	0.225	140	0.181	3179	X-RAY DIFFRACTION	97.3599
2.021-2.119	0.2	145	0.182	3063	X-RAY DIFFRACTION	97.7751
2.119-2.233	0.191	147	0.165	2872	X-RAY DIFFRACTION	97.2616
2.233-2.368	0.179	144	0.156	2700	X-RAY DIFFRACTION	97.1975
2.368-2.53	0.18	144	0.157	2474	X-RAY DIFFRACTION	94.4444
2.53-2.731	0.196	106	0.161	2305	X-RAY DIFFRACTION	94.5861
2.731-2.989	0.204	103	0.163	2227	X-RAY DIFFRACTION	98.687
2.989-3.338	0.181	111	0.169	1987	X-RAY DIFFRACTION	98.5439
3.338-3.846	0.167	93	0.164	1761	X-RAY DIFFRACTION	98.1472
3.846-4.692	0.144	67	0.158	1454	X-RAY DIFFRACTION	95.6604
4.692-6.555	0.187	56	0.187	1170	X-RAY DIFFRACTION	97.9233
6.555-23.508	0.239	18	0.198	657	X-RAY DIFFRACTION	95.2045

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