PDB-7uaw: Structure of Clostridium botulinum prophage Tad1 in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 7uaw

Title

Structure of Clostridium botulinum prophage Tad1 in complex with 1''-2' gcADPR

Components

ABC transporter ATPase

Keywords

VIRAL PROTEIN / Anti-Thoeris / Immune Evasion / signal sequestration

Function / homology

Chem-MF6 / ABC transporter ATPase

Function and homology information

Biological species

Clostridium botulinum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.72 Å

Authors

Lu, A. / Leavitt, A. / Yirmiya, E. / Amitai, G. / Garb, J. / Morehouse, B.R. / Hobbs, S.J. / Sorek, R. / Kranzusch, P.J.

Funding support

1items

Citation

Journal: Nature / Year: 2022
Title: Viruses inhibit TIR gcADPR signalling to overcome bacterial defence.
Authors: Leavitt, A. / Yirmiya, E. / Amitai, G. / Lu, A. / Garb, J. / Herbst, E. / Morehouse, B.R. / Hobbs, S.J. / Antine, S.P. / Sun, Z.J. / Kranzusch, P.J. / Sorek, R.

History

Deposition	Mar 14, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2022	Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 26, 2022	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3	Nov 16, 2022	Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.4	Nov 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7uaw.cif.gz	146.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7uaw.ent.gz	95.7 KB	Display	PDB format
PDBx/mmJSON format	7uaw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7uaw_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7uaw_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7uaw_validation.xml.gz	15 KB	Display
Data in CIF	7uaw_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ua/7uaw ftp://data.pdbj.org/pub/pdb/validation_reports/ua/7uaw	HTTPS FTP

-
Related structure data

Related structure data	7uavC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ABC transporter ATPase

B: ABC transporter ATPase

hetero molecules

29.7 kDa, 2 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)	123.976, 123.976, 112.533
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32
Space group name Hall	R32"
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x-y,-y,-z #5: -x,-x+y,-z #6: y,x,-z #7: x+1/3,y+2/3,z+2/3 #8: -y+1/3,x-y+2/3,z+2/3 #9: -x+y+1/3,-x+2/3,z+2/3 #10: x-y+1/3,-y+2/3,-z+2/3 #11: -x+1/3,-x+y+2/3,-z+2/3 #12: y+1/3,x+2/3,-z+2/3 #13: x+2/3,y+1/3,z+1/3 #14: -y+2/3,x-y+1/3,z+1/3 #15: -x+y+2/3,-x+1/3,z+1/3 #16: x-y+2/3,-y+1/3,-z+1/3 #17: -x+2/3,-x+y+1/3,-z+1/3 #18: y+2/3,x+1/3,-z+1/3

Components on special symmetry positions

ID	Model	Components
1	1	A-409- HOH

#1: Protein	ABC transporter ATPase Mass: 14331.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: FDB51_07880 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A846JTD7
#2: Chemical	ChemComp-MF6 / (1S,3R,4R,6R,9S,11R,14R,15S,16R,18R)-4-(6-amino-9H-purin-9-yl)-9,11,15,16,18-pentahydroxy-2,5,8,10,12,17-hexaoxa-9lambda~5~,11lambda~5~-diphosphatricyclo[12.2.1.1~3,6~]octadecane-9,11-dione / 1'-2' gcADPR Mass: 541.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₁N₅O₁₃P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.77 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 5.0, 1% PEG-6000, and 300 uM gcADPR

-
Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.72→48.45 Å / Num. obs: 35067 / % possible obs: 99.24 % / Redundancy: 3.9 % / R_merge(I) obs: 0.149 / Net I/σ(I): 6.8
Reflection shell	Resolution: 1.72→1.75 Å / Num. unique obs: 1759 / CC_1/2: 0.737 / R_pim(I) all: 0.566

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: D_1000263859

Resolution: 1.72→48.45 Å / SU ML: 0.2121 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1979	1999	5.7 %
R_work	0.1653	33068	-
obs	0.1671	35067	99.24 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 34.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.72→48.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2076	0	0	273	2349

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0133	2110
X-RAY DIFFRACTION	f_angle_d	1.4297	2842
X-RAY DIFFRACTION	f_chiral_restr	0.0841	306
X-RAY DIFFRACTION	f_plane_restr	0.0079	362
X-RAY DIFFRACTION	f_dihedral_angle_d	14.1576	800

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 (%)
1.72-1.76	0.4147	135	0.3751	2229	X-RAY DIFFRACTION	94.64
1.76-1.81	0.3722	142	0.3069	2337	X-RAY DIFFRACTION	99.56
1.81-1.86	0.2796	141	0.2588	2353	X-RAY DIFFRACTION	99.88
1.86-1.92	0.2972	144	0.2261	2379	X-RAY DIFFRACTION	99.76
1.92-1.99	0.2494	143	0.2024	2353	X-RAY DIFFRACTION	99.76
1.99-2.07	0.2403	142	0.1938	2363	X-RAY DIFFRACTION	99.84
2.07-2.17	0.2063	143	0.1721	2349	X-RAY DIFFRACTION	99.76
2.17-2.28	0.2234	141	0.1657	2343	X-RAY DIFFRACTION	99.68
2.28-2.42	0.1968	144	0.1646	2381	X-RAY DIFFRACTION	99.61
2.42-2.61	0.1853	143	0.1644	2374	X-RAY DIFFRACTION	99.49
2.61-2.87	0.2119	143	0.1622	2357	X-RAY DIFFRACTION	98.93
2.87-3.29	0.1752	143	0.1511	2370	X-RAY DIFFRACTION	99.25
3.29-4.14	0.1781	145	0.1404	2409	X-RAY DIFFRACTION	99.8
4.15-48.45	0.159	150	0.1441	2471	X-RAY DIFFRACTION	99.47

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	1.1990668538	-0.286988677215	-0.110695899524	1.6493125357	-0.889847388346	1.77752008305	0.0997009747761	0.0765434398385	-0.0699450542127	-0.0871955954017	0.157596400601	0.306875524084	0.125437976673	-0.0848793222835	-0.330353669302	0.292220088231	0.0229747066978	-0.00697786846961	0.284405988103	-0.00265370437423	0.420641901818	-24.6045322732	5.78851747834	-34.4350706983
2	1.98158810585	1.17364651504	-0.885396746791	2.38556824146	-4.2756190757	9.07384765186	-0.0652197411889	0.358171092733	0.0687643566344	0.148772571089	0.0665293906903	0.053258179185	-0.0769341852788	-0.285266853936	-0.0185465626059	0.256198612303	0.023354567144	-0.0219327758398	0.329542710973	-0.00499493919742	0.427963310067	-24.640397878	13.3408969306	-37.0739108458
3	2.30932176312	0.245641037918	-0.929818116269	1.43863280125	-0.560372483021	3.25768772938	-0.0620444734818	0.381702535899	0.107527973851	-0.226818858464	0.0402021052269	0.112839890165	0.00509745493775	-0.0407740178545	0.0052437570204	0.295897686113	0.040412534944	-0.00222021989546	0.347958248788	0.044885604762	0.32948772569	-19.778231045	17.9366019666	-41.3826158288
4	4.30288065953	0.0978471841043	1.13587809158	3.2538065248	-0.198337618882	2.53880456683	0.286386215025	-0.737811215189	-0.460841165919	0.0995324532698	0.152281325463	0.971655002678	0.211769130486	-0.71165731115	0.0114841494128	0.349893485358	0.0204891869211	0.0145897053656	0.526710938901	0.0811817087386	0.607369105373	-37.2880086749	13.9082700061	-27.2795311406
5	3.99052092694	0.877611892682	-1.81078966761	1.67152708997	-0.909817037411	2.11301435258	0.495695734955	0.377978554754	0.471431428197	0.0488910820693	-0.160906092271	0.547674663763	-0.585733046273	-0.214543153774	-0.0772257533455	0.284673451496	0.0476630652233	-0.000939702452899	0.304899164155	0.0302275666868	0.431536568321	-18.7735596196	23.2754898162	-36.802723905
6	4.08567806298	0.749063334467	-1.81610783393	3.11018558337	-0.619505848232	1.33729467937	0.102364313049	0.491606227021	0.588453553735	-0.408041492068	-0.142635090921	-0.311770414049	-0.177805631279	0.126722596082	0.0460137434925	0.379348806123	0.0219201916133	0.042839116253	0.365963611275	0.106850609238	0.480267191631	-9.03274061753	29.8357236634	-41.8035153721
7	1.52072584675	-0.153588526906	0.170826813943	1.78696213729	-0.200670063399	1.61604007775	0.0729731464948	-0.217641182265	0.116251537055	0.237691547793	-0.101951300283	-0.0588702115883	0.0348955990365	0.234434666345	0.0199765144614	0.295439902165	0.00690155071438	0.000637991278897	0.325148782215	-0.0271877548038	0.276940068626	-11.2734725367	12.6450314806	-20.0596236184
8	1.6411832266	0.206658633758	-0.749982033528	1.01968038517	-0.490969144079	1.86513071137	-0.0182772304957	-0.00816483681565	0.182428952857	-0.0320950039315	0.0635458166993	-0.148175441038	0.144059233641	0.073343920903	-0.0704556050568	0.252630052126	0.0284925643866	-0.0268555611541	0.300304344039	-0.016770893671	0.317965508256	-1.46472350247	11.9123444647	-30.143370083
9	3.82082282896	-2.48148033224	-0.477115208836	2.02708613222	-0.651283161779	2.31440245757	0.0538978233542	0.926377093417	0.296066803529	-0.525743536415	-0.164125614814	0.0649819919424	-0.0476789624323	-0.059633601468	-0.110021531294	0.374024171663	0.0223145287746	0.0994820770761	0.441297597677	0.131138169118	0.514358858495	2.05301259019	23.8882251998	-45.4502005678
10	2.25980035655	-0.343014686709	-0.0876129026307	1.48675970045	-0.0900681909629	1.62102272263	0.145909335055	-0.21850349348	0.35583127453	0.203213804009	-0.0337407164619	0.208892722267	-0.280143904386	0.03682402606	-0.136963015428	0.363202352026	-0.00828061724811	0.0213705944761	0.338611794466	-0.0277986170789	0.489909207629	-3.73080526679	24.8551216194	-24.6183890101
11	2.52325222287	0.953070029625	-0.335004482235	2.06388613737	0.25007226522	2.2379755266	0.158883306905	-0.0903352359071	0.701388060119	0.392774887463	0.0726292704366	0.149427650023	-0.761797991672	-0.0561082071429	-0.168084396952	0.406173397624	0.0341536995224	0.0404649574666	0.319028129073	-0.0638334437526	0.468483151066	-14.0424319396	27.7675654398	-23.1373752332
12	2.78988035134	1.2603171919	-0.102285502672	4.71447431902	-0.281480194004	1.41756253629	0.0759469943137	-0.19694049144	0.582177154205	0.456469619051	-0.0226248212972	0.582750021077	-0.12358504585	-0.147519128708	-0.0339912188537	0.308934584922	0.0575185742467	0.0542668998773	0.349263033031	-0.0539615190497	0.498585338406	-24.9984501431	16.1363307927	-18.9328196343
13	2.01626710418	-0.151508546126	-0.436586150082	0.97859028983	-0.466105224409	1.73255573576	0.103895437327	0.212712154398	0.116854082693	-0.0337456720913	0.0130108428134	0.074613733626	0.0150579154659	0.05949634177	-0.148533863968	0.256407268943	0.0164329014866	-0.00464230459049	0.274002585531	0.00360072962078	0.290454647128	-14.7865870367	12.7685585419	-35.2735280997
14	1.39445922017	0.426050822366	-0.932674130117	1.80783164694	-0.559934096046	1.89789280108	-0.0188280731777	-0.0446463802759	-0.144706457585	-0.0022006717653	0.00684186234149	-0.0556540142748	0.146763262782	0.110802269209	-0.00921598280345	0.276177069423	0.0336351943988	-0.00273579054043	0.275646645845	-0.00395087776624	0.295521329669	-11.7874627989	2.41947449678	-28.9228925255
15	1.83170880292	-1.1146691715	-0.273511490516	3.58629643759	0.0972452934167	2.65324242275	0.165759037374	-0.641836965323	0.248829467145	0.736622546559	0.0110959823121	0.0247891317237	0.12851604448	-0.190702497973	-0.105349639122	0.424681545815	0.0223677388887	0.114775478605	0.451390630266	0.0842497338515	0.415361468871	-23.7018683672	-0.133310232713	-13.4075988433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 19 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 20 through 35 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 36 through 46 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 47 through 56 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 57 through 67 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 68 through 89 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 90 through 115 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 116 through 124 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 13 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 14 through 46 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 47 through 61 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 62 through 89 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 90 through 115 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 116 through 124 )

-
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://pdbjlvh1.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

-
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

-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

-
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