PDB-9ntn: Structure of Cap10-CdnD complex containing NDG modification

ID or keywords:

Entry

Database: PDB / ID: 9ntn

Title

Structure of Cap10-CdnD complex containing NDG modification

Components

Cap10
CdnD

Keywords

ANTIVIRAL PROTEIN / CD-NTase / QueC / CBASS

Function / homology

Chem-2KA / COENZYME A

Function and homology information

Biological species

Hyphomicrobiales (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.43 Å

Authors

Wassarman, D.R. / Pfaff, P. / Paulo, J.A. / Gygi, S.P. / Shokat, K.M. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2025
Title: Deazaguanylation is a nucleobase-protein conjugation required for type IV CBASS immunity.
Authors: Wassarman, D.R. / Pfaff, P. / Paulo, J.A. / Gygi, S.P. / Shokat, K.M. / Kranzusch, P.J.

History

Deposition	Mar 18, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ntn.cif.gz	562.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9ntn.ent.gz	413 KB	Display	PDB format
PDBx/mmJSON format	9ntn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nt/9ntn ftp://data.pdbj.org/pub/pdb/validation_reports/nt/9ntn	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Cap10

B: Cap10

G: CdnD

H: CdnD

hetero molecules

146 kDa, 4 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)	70.459, 82.920, 231.779
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Cap10 Mass: 37446.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphomicrobiales (bacteria) / Production host: Escherichia coli BW25113 (bacteria)
#2: Protein	CdnD Mass: 34453.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphomicrobiales (bacteria) / Production host: Escherichia coli BW25113 (bacteria)
#3: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#4: Chemical	ChemComp-2KA / 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid Mass: 194.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆N₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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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: 50.13 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES-KOH pH 7.5, 0.3 M calcium acetate, 10% PEG-8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2024
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.43→33.87 Å / Num. obs: 52191 / % possible obs: 99.28 % / Redundancy: 13.7 % / B_iso Wilson estimate: 52.94 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.3809 / R_pim(I) all: 0.1061 / R_rim(I) all: 0.3956 / Net I/σ(I): 5.28
Reflection shell	Resolution: 2.43→2.47 Å / Redundancy: 13.9 % / R_merge(I) obs: 3.675 / Mean I/σ(I) obs: 0.36 / Num. unique obs: 2671 / CC_1/2: 0.348 / CC star: 0.718 / R_pim(I) all: 1.017 / R_rim(I) all: 3.814 / % possible all: 94.33

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
Coot	0.9.8.95	model building
AutoProcess	1.0.5	data processing
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.43→33.87 Å / SU ML: 0.4644 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2777	2613	5.03 %
R_work	0.2352	49347	-
obs	0.2373	51960	99.23 %

Solvent computation

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

Displacement parameters

B_iso mean: 67.59 Å²

Refinement step

Cycle: LAST / Resolution: 2.43→33.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9641	0	130	171	9942

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	9970
X-RAY DIFFRACTION	f_angle_d	0.7859	13477
X-RAY DIFFRACTION	f_chiral_restr	0.0412	1467
X-RAY DIFFRACTION	f_plane_restr	0.0078	1743
X-RAY DIFFRACTION	f_dihedral_angle_d	14.1038	3781

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 (%)
2.43-2.47	0.4746	121	0.4556	2421	X-RAY DIFFRACTION	94.32
2.47-2.52	0.5334	145	0.4237	2494	X-RAY DIFFRACTION	96.31
2.52-2.57	0.4221	135	0.3821	2469	X-RAY DIFFRACTION	97.97
2.57-2.62	0.3927	133	0.346	2551	X-RAY DIFFRACTION	98.46
2.62-2.69	0.351	113	0.3185	2605	X-RAY DIFFRACTION	99.31
2.69-2.75	0.2956	131	0.3065	2590	X-RAY DIFFRACTION	99.82
2.75-2.83	0.3842	158	0.3019	2567	X-RAY DIFFRACTION	99.78
2.83-2.91	0.2971	136	0.2917	2578	X-RAY DIFFRACTION	99.89
2.91-3	0.3292	126	0.2873	2597	X-RAY DIFFRACTION	99.89
3-3.11	0.3136	145	0.2836	2617	X-RAY DIFFRACTION	99.96
3.11-3.24	0.3396	145	0.2735	2574	X-RAY DIFFRACTION	99.93
3.24-3.38	0.3176	126	0.2464	2608	X-RAY DIFFRACTION	100
3.38-3.56	0.2937	138	0.228	2619	X-RAY DIFFRACTION	100
3.56-3.78	0.2843	145	0.2192	2624	X-RAY DIFFRACTION	99.96
3.78-4.08	0.2707	140	0.2047	2614	X-RAY DIFFRACTION	100
4.08-4.48	0.211	159	0.1798	2628	X-RAY DIFFRACTION	100
4.48-5.13	0.2356	142	0.1857	2670	X-RAY DIFFRACTION	100
5.13-6.46	0.2333	132	0.2209	2707	X-RAY DIFFRACTION	100
6.46-33.87	0.2039	143	0.1838	2814	X-RAY DIFFRACTION	99.6

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	4.37283643805	-0.472899481646	0.74957423802	3.12467135049	-1.61479313681	3.22889894675	-0.0628026428146	0.164372473332	-0.175181773047	0.360096841186	0.0371969958082	-0.14109644326	0.106801960676	0.285240513112	-0.00942376097997	0.470717824022	0.0338019393838	-0.000757222680962	0.271116168042	-0.0682824414075	0.311625909663	-36.028	-10.201	3.882
2	2.82340454617	-0.194344998796	0.182134580413	2.78543729213	-0.744485734617	1.88283534444	-0.0511049384938	0.0878761938185	0.0406631783535	0.222321830662	-0.0183017934246	-0.443856297508	0.117966146032	0.498150763414	0.0831493856119	0.364747118876	0.0464023100312	-0.0291130809429	0.413583985788	-0.020184185413	0.363323711472	-24.869	-2.094	5.385
3	4.54899435314	0.381106566669	-1.5582477355	2.14283519871	-0.152899481031	2.80556920369	-0.00852155982957	0.256075219657	0.289797236509	0.217347650867	0.025079132171	-0.0376128341311	-0.402104611937	-0.0941915174092	-0.0131578023439	0.413635461344	0.0203252745802	-0.0555128645528	0.280185428116	0.00928521270849	0.324831913191	-45.692	8.464	1.27
4	3.69529526956	-1.13200191334	1.24018954742	4.06258115945	-1.10757850403	2.13759042011	-0.0232057184526	-0.335134998821	-0.0569275253569	0.266390599844	0.106085332202	-0.202849056167	0.610507581514	0.173701898382	0.030054234688	0.651440343522	0.14406322167	-0.028585598859	0.485704256616	-0.0397403793323	0.305773480938	-52.541	8.103	34.272
5	1.29475896855	0.0367751759809	-0.178582376931	2.68699166741	0.380400657306	2.69791667	-0.0424626668183	-0.190157694685	-0.177627409077	0.457876787758	-0.0758568974436	0.152332164849	0.72349878142	-0.315590326501	0.0965492567512	0.592266988945	-0.0105947644302	0.0430812300912	0.45065064098	-0.0450526061898	0.377572050782	-63.938	1.609	31.45
6	6.46513312928	-1.52888993214	-1.29446788827	2.96535841746	0.369280269192	2.40933730676	0.00435286381718	-0.140736802104	0.273347268879	-0.0513962662647	0.0109075242037	0.128466965658	-0.179290644925	-0.0168274825846	-0.0402127917368	0.520351416459	0.0906251295927	-0.070813467753	0.353900206239	-0.0444774404465	0.366226138055	-52.685	17.143	17.85
7	1.58473392423	-0.165178416757	-0.410871269114	1.4521886719	2.19769321202	4.11413468782	0.0448299216025	-0.551373517206	-0.113950465692	0.282933817637	0.142677084835	0.405534665823	0.999163300185	-0.245183072592	0.0581277778963	0.631530010145	-0.13613883752	0.103210441359	0.570525556394	-0.0990424412059	0.543604365868	-59.25	-9.478	2.925
8	1.78582863155	-0.417581269272	-0.475666130936	0.871930882405	0.946853397279	5.86171703917	0.163246102193	0.485374976734	0.214498589338	-0.496058274858	-0.139005480809	0.250670405107	-0.529117183205	-0.482084635207	0.050692358424	0.705811281343	0.0870823105425	-0.0375304946242	0.511058745811	0.0755407620465	0.482977109388	-55.291	1.693	-38.486
9	4.06701912626	-0.813495044075	-0.815899043448	2.14195881996	0.189078372291	4.19080424362	0.355962154188	0.484018492103	-0.511699307833	-0.577737617224	-0.0306444705578	-0.133692448443	0.0773303563447	0.276660783143	0.0854528178219	0.663479639555	0.129879271335	0.0459626528304	0.6341217308	-0.0385162916542	0.422719876709	-47.232	-9.711	-42.804
10	3.17821199326	0.0477713576926	-0.166229612029	0.864624575489	-1.30083670112	5.67559490581	0.159764072655	0.384051399083	0.0927485442414	-0.282868961742	-0.378165312482	-0.442930171529	-0.63751942136	0.996880385409	0.23873914847	0.887628872227	-0.00923418700156	0.0133787783748	0.821363911657	0.0591792122496	0.422685950737	-43.484	-4.289	-49.59
11	4.40869926343	-1.58162462439	-1.43387332088	5.87047413093	-0.126472359732	6.12390507792	-0.293753202203	-0.478941772094	-0.85717437734	-0.334466991048	0.135321214822	-0.523874661546	0.592769918412	0.863972479023	0.306719338314	0.935884142018	0.181178297178	0.0707642641489	0.831573085399	0.0752685871751	0.48929625953	-46.504	-20.866	-42.117
12	1.89392927925	-0.349733727038	-0.564446097221	4.88739567599	1.37364994148	4.33650100084	-0.0384906075813	0.539554936633	0.0145017752772	-0.502810029105	-0.0291861802219	0.101167777466	-0.0999214077802	-0.125825860041	0.0364150196245	0.451084310726	0.0203282427357	-0.0189137990195	0.409246991398	0.0329939702718	0.307875730167	-53.592	-9.576	-29.684
13	2.41214620148	-0.918927254927	-1.03129933558	5.97717459672	1.63540052776	3.55949578533	-0.294931139951	-0.486048435434	0.257111728204	0.204624877308	0.432598815458	0.474804653379	0.261834260006	-0.849495633869	0.101856121678	0.470805818565	-0.00535803434643	0.0121766086509	0.550196821929	0.0102109614742	0.359071268417	-58.281	-9.524	-20.298
14	2.22413599654	-0.883700160054	-0.66468058655	6.73368630715	1.81100812665	4.2195817149	-0.34520448436	-0.113307561103	-0.090874365958	-0.052960897791	0.404487814233	-0.0106249053485	0.261264036921	0.240280140433	-0.0225776601302	0.300962585874	0.00569885724467	0.0463245492073	0.384859810368	0.0541923625831	0.303139247403	-49.671	-12.146	-19.516
15	1.28192391665	0.671491789461	-1.61174412825	3.01835993065	2.83120291624	7.17696155515	-0.133129509741	-0.0415320103338	0.0777469677987	1.37728916248	0.117835156182	-1.28291041198	0.748051273804	0.627218559454	-0.0558428662831	0.572466429887	0.0929712665546	-0.195540996864	0.93380058687	-0.255761070471	0.764869894224	-32.214	15.256	29.405
16	1.36246643183	-1.02225077129	-0.449175666601	6.25335713966	3.23277181623	4.14628703076	-0.000733245654198	-0.244625496711	1.58630883332	-1.37461911376	0.973249745767	-0.445693887799	-1.72271124281	0.759159395717	-0.943398284669	0.913298205502	-0.120908310895	0.0131064419163	0.587546451359	-0.0853821330771	1.33099731704	-48.949	50.334	34.431
17	1.49581612899	-0.983966299939	-0.51317333019	0.908831521978	-0.336943796807	3.11907969099	-0.0427463812599	-0.216467725256	0.932099337296	-0.0796933157516	-0.5375914523	1.22061157529	-0.0571643718427	-0.172997628967	0.706868076488	0.673001539497	0.0614687704077	0.0193128699122	0.664619357392	-0.222065656354	1.27181789428	-51.315	50.222	46.842
18	2.90073690759	1.68565013297	0.807462612185	2.35679784445	1.92415272003	1.63163111987	0.0796592184051	-1.19001196639	1.1870386251	0.874965813845	-0.234162550114	0.48979456915	-0.532336591873	-0.680758440225	-0.211947335034	1.22251729908	-0.0253981326714	0.494831283886	1.11088466312	-0.497329508779	1.56379357766	-56.654	54.773	58.347
19	4.18349955845	-0.55977598411	1.63004205578	2.18806971158	-0.339347483747	4.52209462974	-0.163999686205	-0.944232208435	1.16498985618	0.885081490166	0.161493988612	0.566198453017	-0.302502581474	-0.587281235729	-0.112990626675	1.00414463473	0.0424079034581	0.282801859232	0.816203569361	-0.398545220781	1.51123006957	-57.049	52.61	54.143
20	0.38107880015	0.969144357159	-0.490291329127	3.63444120533	-1.73114886212	8.65223811982	0.381705814462	-1.23111049168	0.778042496206	1.51293880746	-0.266278632943	0.192314126024	0.133195164676	0.604885527277	-0.53841113318	1.20968189871	-0.253006862993	0.288797393379	1.04267695847	-0.415449460067	0.923352747419	-43.827	45.403	55.792
21	3.66611997625	1.00969862231	1.58556031386	7.4820343534	0.174984885077	7.20225243334	0.105573683712	-0.0294461784124	0.53800063566	0.763901101116	0.173732179332	-0.285283449913	0.492244628129	0.606382056114	-0.30438840477	0.567212338605	0.0309021434011	0.0343682049504	0.514725660523	-0.244169752797	0.782150301231	-43.876	36.265	43.287
22	3.17481336614	-3.32388436278	-0.783312705869	4.06893987195	-0.0952182436117	1.49534314633	0.107652709465	-1.45402359484	1.14869215404	1.58139161154	-0.000255005895826	-1.03169997216	-0.460818593902	-0.34742258227	-0.0151353371318	1.5972947094	0.0438431106749	-0.338853769011	1.28810045789	-0.42066494614	0.930301082356	-40.076	31.599	57.935
23	2.71011711832	-0.773254056456	-0.317166338928	3.68895539156	0.637144380053	2.74076525881	-0.139832644968	-0.00290018571844	0.169342992126	0.62378543232	0.0990953963472	0.106143782583	0.392523603629	-0.130484585019	0.0280234996193	0.521290063372	0.0599079184063	-0.0218562021249	0.420034964697	-0.109085384987	0.460631588927	-48.77	27.809	36.107

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:109 )	A	1 - 109
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 110:258 )	A	110 - 258
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 259:327 )	A	259 - 327
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 1:88 )	B	1 - 88
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 89:258 )	B	89 - 258
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 259:330 )	B	259 - 330
7	X-RAY DIFFRACTION	7	( CHAIN G AND RESID 5:29 )	G	5 - 29
8	X-RAY DIFFRACTION	8	( CHAIN G AND RESID 30:86 )	G	30 - 86
9	X-RAY DIFFRACTION	9	( CHAIN G AND RESID 87:112 )	G	87 - 112
10	X-RAY DIFFRACTION	10	( CHAIN G AND RESID 113:158 )	G	113 - 158
11	X-RAY DIFFRACTION	11	( CHAIN G AND RESID 159:178 )	G	159 - 178
12	X-RAY DIFFRACTION	12	( CHAIN G AND RESID 179:230 )	G	179 - 230
13	X-RAY DIFFRACTION	13	( CHAIN G AND RESID 231:255 )	G	231 - 255
14	X-RAY DIFFRACTION	14	( CHAIN G AND RESID 256:311 )	G	256 - 311
15	X-RAY DIFFRACTION	15	( CHAIN H AND RESID 5:29 )	H	5 - 29
16	X-RAY DIFFRACTION	16	( CHAIN H AND RESID 30:65 )	H	30 - 65
17	X-RAY DIFFRACTION	17	( CHAIN H AND RESID 66:92 )	H	66 - 92
18	X-RAY DIFFRACTION	18	( CHAIN H AND RESID 93:127 )	H	93 - 127
19	X-RAY DIFFRACTION	19	( CHAIN H AND RESID 128:169 )	H	128 - 169
20	X-RAY DIFFRACTION	20	( CHAIN H AND RESID 170:192 )	H	170 - 192
21	X-RAY DIFFRACTION	21	( CHAIN H AND RESID 193:255 )	H	193 - 255
22	X-RAY DIFFRACTION	22	( CHAIN H AND RESID 256:277 )	H	256 - 277
23	X-RAY DIFFRACTION	23	( CHAIN H AND RESID 278:311 )	H	278 - 311

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