PDB-7r65: Crystal structure of a bacterial cyclic UMP synthase from Burkhol...

ID or keywords:

Entry

Database: PDB / ID: 7r65

Title

Crystal structure of a bacterial cyclic UMP synthase from Burkholderia cepacia LK29

Components

Adenylate/guanylate cyclase

Keywords

TRANSFERASE /

Cyclic nucleotide /

nucleotidyltransferase / bacteriophage-defense / Pycsar

Function / homology

cyclic nucleotide biosynthetic process / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / intracellular signal transduction / Adenylate/guanylate cyclase

Function and homology information

Biological species

Burkholderia cepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.45 Å

Authors

Morehouse, B.R. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Cell / Year: 2021
Title: Cyclic CMP and cyclic UMP mediate bacterial immunity against phages.
Authors: Tal, N. / Morehouse, B.R. / Millman, A. / Stokar-Avihail, A. / Avraham, C. / Fedorenko, T. / Yirmiya, E. / Herbst, E. / Brandis, A. / Mehlman, T. / Oppenheimer-Shaanan, Y. / Keszei, A.F.A. / ...

History

Deposition	Jun 22, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 27, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 24, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7r65.cif.gz	463.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7r65.ent.gz	326.5 KB	Display	PDB format
PDBx/mmJSON format	7r65.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/r6/7r65 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/7r65	HTTPS FTP

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Related structure data

Similar structure data	7r65-2 5veu-9 5x4j-d 4cd1-d 1lpn-d 5bk6-2 4k9x-d 3fzh-1 6da2-d 4s3n-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#251 - Nov 2020 Adenylyl Cyclase similarity (4) #133 - Jan 2011 Nitric Oxide Synthase similarity (4) #58 - Oct 2004 G Proteins similarity (4)

Deposited unit

A: Adenylate/guanylate cyclase

B: Adenylate/guanylate cyclase

C: Adenylate/guanylate cyclase

D: Adenylate/guanylate cyclase

103 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenylate/guanylate cyclase

B: Adenylate/guanylate cyclase

defined by author&software
Evidence: gel filtration
51.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Adenylate/guanylate cyclase

D: Adenylate/guanylate cyclase

defined by author&software
Evidence: gel filtration
51.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.145, 66.758, 92.350
Angle α, β, γ (deg.)	90.000, 111.262, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Adenylate/guanylate cyclase Mass: 25769.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cepacia (bacteria) / Gene: VL15_12785 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J5ZXG5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1099 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.32 Å³/Da / Density % sol: 46.92 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M ammonium acetate, 0.1 M HEPES-KOH pH 7.5, and 29% PEG-3350

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.45→48.96 Å / Num. obs: 167231 / % possible obs: 99.7 % / Redundancy: 48.9 % / B_iso Wilson estimate: 16.22 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.029 / Net I/σ(I): 16.8
Reflection shell	Resolution: 1.45→1.47 Å / Redundancy: 40.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7966 / CC_1/2: 0.181 / R_pim(I) all: 0.872 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.45→45.22 Å / SU ML: 0.1504 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1976	2000	1.2 %
R_work	0.1772	164623	-
obs	0.1774	166623	99.43 %

Solvent computation

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

Displacement parameters

B_iso mean: 21.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→45.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7208	0	0	1099	8307

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	7441
X-RAY DIFFRACTION	f_angle_d	0.638	10136
X-RAY DIFFRACTION	f_chiral_restr	0.0665	1141
X-RAY DIFFRACTION	f_plane_restr	0.0038	1280
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7253	2650

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 (%)
1.45-1.48	0.2721	135	0.2612	11109	X-RAY DIFFRACTION	94.27
1.48-1.52	0.2128	142	0.2294	11675	X-RAY DIFFRACTION	99.75
1.52-1.57	0.2293	142	0.2052	11758	X-RAY DIFFRACTION	99.76
1.57-1.62	0.2182	144	0.1935	11759	X-RAY DIFFRACTION	99.82
1.62-1.68	0.1984	142	0.1842	11767	X-RAY DIFFRACTION	99.83
1.68-1.74	0.2167	143	0.1848	11784	X-RAY DIFFRACTION	99.96
1.74-1.82	0.2124	144	0.1833	11755	X-RAY DIFFRACTION	99.94
1.82-1.92	0.2318	143	0.1824	11818	X-RAY DIFFRACTION	99.77
1.92-2.04	0.1954	143	0.171	11726	X-RAY DIFFRACTION	99.39
2.04-2.2	0.1873	143	0.1687	11818	X-RAY DIFFRACTION	99.96
2.2-2.42	0.2336	144	0.175	11865	X-RAY DIFFRACTION	99.92
2.42-2.77	0.1929	144	0.1763	11825	X-RAY DIFFRACTION	99.82
2.77-3.49	0.1899	144	0.1774	11890	X-RAY DIFFRACTION	99.94
3.49-45.22	0.1707	147	0.1628	12074	X-RAY DIFFRACTION	99.81

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	0.374752395493	-0.0345806683383	0.00662315390681	0.136679062239	0.04092666776	0.799845724128	0.0207268895058	-0.0123930045194	0.0520476093681	-0.00307647239797	0.0141862263945	-0.00401983025672	-0.109411925961	0.0440522138245	0.0379659102738	0.132889087991	-0.0190590003152	0.0154636046688	0.0785207862483	-0.0158544890362	0.115775420368	10.1005933257	38.5497831926	-11.0651332536
2	0.767414794516	0.162537724572	0.0224244049018	0.716926692486	0.157089174009	1.18177967223	0.0313332707536	0.041735945872	-0.0288057895283	-0.048798343073	0.0396380041972	0.0333573308002	-0.100025002937	-0.0756989128618	0.144012105383	0.102046528732	0.0257277034023	0.00232424749021	0.0737180165364	-0.00482685378877	0.0996023183511	-5.50258736992	36.3859110825	-11.011065115
3	1.65055410332	0.540418158964	0.104017463357	0.176804472879	0.0270781359421	0.0228333112529	0.124268583183	0.46229565866	0.0360855301386	-0.0378687540204	-0.0786582548025	0.0281581702363	-0.476886534917	-0.509332836834	0.0542273120517	0.31714208187	0.125074478888	0.0142123981129	0.249108313833	0.0521829560657	0.151146748578	-5.07597853473	38.4334976915	-32.7342239347
4	0.142889447744	-0.103250323933	0.00166872422132	0.129231908612	0.0914062090709	0.325713373192	0.00748412595173	0.250421521546	0.228111031789	-0.0771099022046	-0.119408657667	-0.0470032088158	-0.19253692227	0.290514942289	-0.000760135554562	0.203112726304	-0.0118156481664	0.0282546077116	0.212698066256	0.0114517043984	0.135317317735	14.5264804613	31.5677841258	-33.1777379865
5	-0.00106865292228	-0.015726383215	0.00349104616391	0.203309081722	-0.185632094525	0.160165310866	-0.0370314794152	-0.0775887512594	-0.0241198083441	0.0689783931045	-0.0131992059798	0.0791129402957	-0.0975864920152	-0.118145428469	7.5072227268E-6	0.184452778979	-0.00351753694934	0.0182992683825	0.226938856951	-0.00193922577828	0.129615634315	11.8963112452	29.9244375893	-1.50226699977
6	0.15976551039	-0.252001948187	0.0724435194752	0.37755069151	-0.142991961993	0.360056245063	-0.00635451622317	0.0236570220651	0.0613565567467	-0.0234043667123	-0.0378437033533	0.0028143531713	-0.0520200411242	0.0202125414086	-4.95556578235E-5	0.118512231752	-0.0269255233911	0.0131780168537	0.161728376957	-0.0150431015435	0.111801237694	19.802518226	33.1519287692	-8.61319458002
7	0.260647349227	-0.21669740293	-0.0411951855967	0.370097321706	-0.169550599948	0.228013721459	-0.022054420333	-0.086061031068	-0.00614703721553	0.0721432378833	0.0646118564182	-0.0895080862289	0.0502942026241	0.103905672802	-0.000543580430275	0.117419283162	-0.000940512045531	0.006333428369	0.179961720393	-0.00842198221428	0.0925843767389	22.8220863702	26.5239828151	-0.931640462633
8	0.411827582162	-0.00744755819066	0.202201004923	0.054785020985	-0.158187407068	0.389870546529	0.0677095537371	-0.0809913132665	0.0391134022267	-0.00384024976203	-0.0175773777315	0.110248038519	-0.145275924224	-0.0159766009844	1.78674392739E-5	0.172913241164	-0.0198669614322	0.0236238910611	0.157020478164	-0.0114428899429	0.117803209023	11.362513783	28.5666892464	-21.3403165794
9	0.288451622415	-0.172942991258	0.0112698796266	0.802519268964	0.00371109728027	0.785745516234	0.0931263622272	-0.121512650403	-0.231649918659	0.0456891516774	-0.0829518141177	-0.100372282738	0.4168323671	0.000315300853092	-0.000822900144443	0.209325810853	5.62348143889E-5	-0.0111927286737	0.158743189794	0.0160005740066	0.157180814839	22.6292496255	13.0862334081	-9.040339054
10	0.529068190638	-0.0289982468052	-0.00205142997356	0.108858315021	0.0600720028062	0.572815457131	-0.00186105515889	-0.0181716914483	-0.098319520152	-0.0178850736769	-0.000681957534228	0.00393221239486	0.0380488026038	0.0136228565788	-0.000779558247652	0.0958760850427	0.00194721893518	0.00559890100628	0.0740123933487	0.0168162040918	0.144717018862	43.8106474486	27.745190762	-39.8681987541
11	1.04379706657	0.0513753394098	0.145001332658	0.325685064589	0.00919802271275	0.588346101147	-0.0170518926	0.0492805249713	-0.14451183303	0.000902239820106	0.0656941187273	0.105247444604	-0.0511449255726	-0.0790845543867	0.0120608106898	0.121221573306	0.025202691175	-0.00339882651745	0.104421075556	-0.00835272812871	0.135495806256	45.2244289267	30.7459786574	-56.1808673782
12	1.09128040685	-0.236248384516	-0.0843778260858	0.604740618385	-0.198823842748	0.87897639516	0.024277282845	0.0991605623091	-0.0970794100263	-0.0761658982405	-0.00577203419578	-0.0300048165688	-0.0255186438965	0.0637569041485	0.012915042429	0.1109989185	0.00987587317901	-0.00160239980766	0.0858528310081	-0.029768847113	0.110920904277	56.3704271534	29.3547273265	-51.2779331854
13	0.803179539876	-0.0794918944951	0.247830096904	0.237001989715	0.422439607692	0.503950033209	0.0396275475864	0.117888981362	-0.206543242844	0.0433572054098	-0.028993923974	0.0724787648819	0.16570089679	-0.306830305177	0.049418196749	0.143594455509	-0.00821122730586	-0.0168665560776	0.168891208372	-0.0145120216119	0.173685990139	25.8903427279	32.3909854918	-52.9053681093
14	0.111616389897	0.153296998788	0.0753028008231	0.200607322207	0.109047491635	0.0460829271817	0.0288572959665	0.257961926688	-0.120006733927	-0.0929738219717	0.0170029580887	-0.0820730893737	0.0287012201551	0.170743159335	-0.000139155365902	0.136497011664	-0.00591389174091	0.00666457113884	0.23132858159	-0.00215900257208	0.171901240506	51.1298721222	36.4613948482	-33.5240401202
15	0.342979829684	-0.201227265899	0.162622718186	0.379178383765	0.200219306042	0.134740034599	0.050198609072	0.0572054441661	-0.0545010439869	-0.0830407080342	-0.042461177202	0.0117321980066	0.0638821416356	-0.00262013701344	-4.25472429131E-5	0.113722402189	-0.00132950212732	-9.11246766266E-5	0.158909231208	0.0272091802911	0.154596583699	41.0479075955	33.1545020026	-30.0240790769
16	0.247574286469	0.179622966183	0.0937074390515	0.457683927478	0.343322101604	0.346065270993	-0.0254506952247	-0.0124226650116	-0.0070401106769	0.0637343906592	0.0307326768192	-0.0558013279941	-0.0118765669404	0.0903493027761	0.0028448408146	0.0697420874608	-0.000990202923216	-0.000578588796925	0.159721066779	0.0173517450374	0.114966068874	46.2556718705	39.7723229549	-23.7651529976
17	0.224110298474	0.0652833850947	-0.00940731885228	0.0112771479188	0.0555291776502	0.410955292858	-0.013492311013	0.0229536647724	-0.185373367714	-0.0389094832791	0.00286349355322	-0.0417770530903	0.0394174037871	0.094549619089	-7.71368915413E-6	0.126424760026	-9.66234027436E-5	-0.0059875768016	0.157204144464	0.0235462441121	0.165604768685	34.16512298	37.7163495852	-43.8537350226
18	0.947813017049	-0.0359144179658	0.457982615693	0.891252983425	0.0909765492996	0.395697731817	-0.102182702824	-0.0422771605804	0.3505860276	0.139854041777	-0.0712135015594	0.0181799819561	-0.337311596712	0.113339915589	-0.0113494720427	0.170065890289	-0.0157455038638	-0.023780591014	0.130973002303	0.0117894140171	0.167524777138	39.2650378835	53.2037895814	-27.8911432246

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 85 )	A	A	1 - 85	1 - 88
2	2	chain 'A' and (resid 86 through 229 )	A	A	86 - 229	89 - 233
3	3	chain 'B' and (resid 1 through 16 )	B	B	1 - 16	1 - 16
4	4	chain 'B' and (resid 17 through 45 )	B	B	17 - 45	17 - 46
5	5	chain 'B' and (resid 46 through 64 )	B	B	46 - 64	47 - 65
6	6	chain 'B' and (resid 65 through 106 )	B	B	65 - 106	66 - 108
7	7	chain 'B' and (resid 107 through 149 )	B	B	107 - 149	109 - 151
8	8	chain 'B' and (resid 150 through 179 )	B	B	150 - 179	152 - 181
9	9	chain 'B' and (resid 180 through 229 )	B	B	180 - 229	182 - 231
10	10	chain 'C' and (resid 1 through 85 )	C	C	1 - 85	1 - 88
11	11	chain 'C' and (resid 86 through 149 )	C	C	86 - 149	89 - 153
12	12	chain 'C' and (resid 150 through 229 )	C	C	150 - 229	154 - 233
13	13	chain 'D' and (resid 1 through 45 )	D	D	1 - 45	1 - 45
14	14	chain 'D' and (resid 46 through 64 )	D	D	46 - 64	46 - 64
15	15	chain 'D' and (resid 65 through 106 )	D	D	65 - 106	65 - 106
16	16	chain 'D' and (resid 107 through 149 )	D	D	107 - 149	107 - 149
17	17	chain 'D' and (resid 150 through 179 )	D	D	150 - 179	150 - 179
18	18	chain 'D' and (resid 180 through 229 )	D	D	180 - 229	180 - 229

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