PDB-9c63: High resolution structure of cytidine deaminase T6S toxin from Ps...

ID or keywords:

Entry

Database: PDB / ID: 9c63

Title

High resolution structure of cytidine deaminase T6S toxin from Pseudomonas syringae

Components

SsdA

Keywords

TOXIN / DNA binding / deaminase / TOXIN-DNA complex

Function / homology

: / Single-strand DNA deaminase toxin A, C-terminal / Class I prePAAR effector Rhs1 motif / PAAR motif / PAAR motif / membrane / PHOSPHATE ION / Rhs protein

Function and homology information

Biological species

Pseudomonas syringae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.34 Å

Authors

Yin, L. / Shi, K. / Aihara, H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	P01-CA234228 NCI	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM118047	United States

Citation

Journal: Nat Commun / Year: 2025
Title: Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA.
Authors: Yin, L. / Chen, Y. / Shi, K. / Barreto Duran, E. / Harris, R.S. / Aihara, H.

History

Deposition	Jun 7, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9c63.cif.gz	145.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9c63.ent.gz	112.5 KB	Display	PDB format
PDBx/mmJSON format	9c63.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9c63_validation.pdf.gz	464.8 KB	Display	wwPDB validaton report
Full document	9c63_full_validation.pdf.gz	467 KB	Display
Data in XML	9c63_validation.xml.gz	20.7 KB	Display
Data in CIF	9c63_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c6/9c63 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/9c63	HTTPS FTP

-
Related structure data

Related structure data	9c64C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SsdA

B: SsdA

hetero molecules

36.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SsdA

hetero molecules

defined by author&software
18.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: SsdA

hetero molecules

defined by author&software
18.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.687, 73.485, 78.061
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 2 molecules AB

#1: Protein	SsdA Mass: 18083.240 Da / Num. of mol.: 2 / Mutation: E348A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q0DAS4

-
Non-polymers , 5 types, 349 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.12 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 1.8 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic pH 8.2

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.335→30.14 Å / Num. obs: 59524 / % possible obs: 93.8 % / Redundancy: 5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.051 / R_pim(I) all: 0.024 / R_rim(I) all: 0.057 / R_sym value: 0.051 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.335→1.41 Å / R_merge(I) obs: 0.796 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2976 / CC_1/2: 0.602 / R_pim(I) all: 0.447 / R_rim(I) all: 0.916 / R_sym value: 0.796

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.34→30.14 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1954	3036	5.1 %
R_work	0.1688	-	-
obs	0.1702	59522	85.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.34→30.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2400	0	18	342	2760

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	13.047	964
X-RAY DIFFRACTION	f_chiral_restr	0.087	353
X-RAY DIFFRACTION	f_plane_restr	0.007	437

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 (%)
1.34-1.36	0.1917	6	0.2373	155	X-RAY DIFFRACTION	5
1.36-1.38	0.351	25	0.2717	677	X-RAY DIFFRACTION	23
1.38-1.4	0.2707	77	0.2536	1404	X-RAY DIFFRACTION	47
1.4-1.43	0.2536	100	0.2394	2059	X-RAY DIFFRACTION	69
1.43-1.45	0.2264	105	0.2267	2414	X-RAY DIFFRACTION	81
1.45-1.48	0.2496	128	0.2246	2615	X-RAY DIFFRACTION	89
1.48-1.52	0.236	144	0.2044	2866	X-RAY DIFFRACTION	95
1.52-1.55	0.2306	148	0.1905	2948	X-RAY DIFFRACTION	99
1.55-1.59	0.1982	165	0.179	2933	X-RAY DIFFRACTION	99
1.59-1.63	0.2043	162	0.1726	2928	X-RAY DIFFRACTION	99
1.63-1.68	0.1864	150	0.1764	2955	X-RAY DIFFRACTION	99
1.68-1.74	0.1869	180	0.1752	2885	X-RAY DIFFRACTION	98
1.74-1.8	0.2408	152	0.179	2958	X-RAY DIFFRACTION	99
1.8-1.87	0.2128	187	0.1908	2933	X-RAY DIFFRACTION	100
1.87-1.96	0.2169	173	0.171	2995	X-RAY DIFFRACTION	99
1.96-2.06	0.1901	149	0.1683	2981	X-RAY DIFFRACTION	99
2.06-2.19	0.1893	195	0.1641	2945	X-RAY DIFFRACTION	99
2.19-2.36	0.1927	151	0.1678	2972	X-RAY DIFFRACTION	99
2.36-2.59	0.2107	169	0.175	2944	X-RAY DIFFRACTION	97
2.59-2.97	0.1996	141	0.1835	2935	X-RAY DIFFRACTION	96
2.97-3.74	0.2014	161	0.155	2951	X-RAY DIFFRACTION	96
3.74-30.14	0.1617	168	0.1476	3033	X-RAY DIFFRACTION	94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.5212	3.381	2.5613	4.9758	5.1737	6.2702	0.0691	-0.0682	-0.0492	0.1876	-0.132	0.1625	0.1927	-0.2263	0.1119	0.0609	0.0121	-0.0033	0.1264	0.0109	0.0859	11.9597	12.3672	42.7662
2	6.3154	-0.6766	2.7465	8.3457	4.8908	5.3491	-0.4709	0.9531	-0.7779	-0.9208	-0.0137	0.2634	0.4281	-0.0937	0.5311	0.5583	0.0459	0.036	0.3657	-0.1235	0.3953	14.6178	-6.6589	28.9013
3	2.0258	-0.0449	-0.5941	7.4151	3.3019	7.2182	0.0142	0.1049	0.0084	0.0003	0.0001	0.2835	0.223	-0.3743	-0.0326	0.1195	-0.0077	-0.031	0.2276	0.0072	0.1188	9.8678	8.8105	31.9591
4	3.091	1.1235	-0.5748	3.1628	-1.0917	4.1759	-0.16	0.5147	0.1032	-0.5275	0.2338	0.2444	0.2544	-0.4634	-0.0813	0.24	0.0238	-0.0244	0.3556	0.0124	0.1354	12.7858	10.7983	21.6738
5	3.6515	-0.998	-0.5473	5.4693	0.7952	4.4927	-0.0591	0.6743	-0.7354	-0.5504	0.349	-0.5885	0.5815	0.3068	-0.2173	0.3435	0.0118	0.1092	0.4026	-0.0836	0.2605	25.4906	7.5376	18.3982
6	1.237	0.5942	0.1108	2.1748	0.2582	2.0889	-0.017	0.1881	0.0214	-0.0894	0.0009	-0.0835	-0.0463	0.0784	0.016	0.0953	0.0209	-0.007	0.1868	0.0163	0.1426	20.3093	15.5471	32.6977
7	6.2429	5.1999	-4.3305	4.4361	-3.5999	3.2461	0.0362	-0.2366	-0.5888	-0.0194	-0.2163	-0.3393	0.4884	0.1739	0.2717	0.2399	-0.0037	-0.0461	0.2264	0.0328	0.215	23.0827	10.3107	46.5017
8	2.9504	2.9466	1.7861	4.5949	3.4888	3.5595	0.029	-0.0123	-0.05	-0.0693	-0.2112	0.3739	0.0462	-0.4792	0.2462	0.1883	-0.0034	0.0084	0.2255	-0.0163	0.1752	-12.9801	14.9694	20.3182
9	2.7342	0.2897	0.8502	7.5343	0.244	5.3623	-0.0389	0.2579	-0.5648	-0.285	-0.0477	-0.0731	0.4248	-0.3325	0.0017	0.1789	-0.0427	0.0151	0.2113	-0.0816	0.2441	-11.8339	3.0343	8.6818
10	2.0741	-0.8665	-0.3909	1.6114	-0.8086	0.8293	0.0609	1.2692	-0.4122	-0.7069	-0.2349	0.5294	0.2921	-0.727	0.0534	0.3324	0.0096	-0.058	0.5617	-0.1194	0.2871	-11.9225	6.8944	0.6672
11	1.5195	-0.9699	-0.9422	1.8321	1.463	3.2487	0.106	0.1108	0.0657	-0.208	-0.0401	-0.1255	-0.2106	0.0447	-0.0456	0.1706	-0.0001	0.0114	0.1329	0.0132	0.1327	-0.4707	14.8685	9.8298

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 255 through 279 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 280 through 289 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 290 through 300 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 301 through 325 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 326 through 340 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 341 through 401 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 402 through 410 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 255 through 279 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 280 through 298 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 299 through 314 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 315 through 408 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 349 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 349 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 349 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi