PDB-4rt0: Structure of the Alg44 PilZ domain from Pseudomonas aeruginosa PA...

ID or keywords:

Entry

Database: PDB / ID: 4rt0

Title

Structure of the Alg44 PilZ domain from Pseudomonas aeruginosa PAO1 in complex with c-di-GMP

Components

Alginate biosynthesis protein Alg44

Keywords

PROTEIN BINDING / PilZ domain / c-di-GMP receptor

Function / homology

Function and homology information

mannuronan synthase / alginate synthase activity / long-chain fatty acid-CoA ligase activity / alginic acid biosynthetic process / Gram-negative-bacterium-type cell wall / cyclic-di-GMP binding / single-species biofilm formation / periplasmic space
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Whitfield, G.B. / Whitney, J.C.

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Dimeric c-di-GMP Is Required for Post-translational Regulation of Alginate Production in Pseudomonas aeruginosa.
Authors: Whitney, J.C. / Whitfield, G.B. / Marmont, L.S. / Yip, P. / Neculai, A.M. / Lobsanov, Y.D. / Robinson, H. / Ohman, D.E. / Howell, P.L.

History

Deposition	Nov 12, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 3, 2015	Group: Database references
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rt0.cif.gz	149.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4rt0.ent.gz	120.7 KB	Display	PDB format
PDBx/mmJSON format	4rt0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4rt0_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	4rt0_full_validation.pdf.gz	2.8 MB	Display
Data in XML	4rt0_validation.xml.gz	20.8 KB	Display
Data in CIF	4rt0_validation.cif.gz	26.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rt/4rt0 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/4rt0	HTTPS FTP

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Related structure data

Related structure data	4rt1C C: citing same article (ref.)
Similar structure data	5rgl-d 4rt1-1 7c6s-d 5rel-d 7l0d-d 5reg-d 5nyo-d 4e9j-2 5rg0-d 3p2t-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	#254 - Feb 2021 Cellulose Synthase similarity (2) #130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: Alginate biosynthesis protein Alg44

B: Alginate biosynthesis protein Alg44

C: Alginate biosynthesis protein Alg44

hetero molecules

41.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alginate biosynthesis protein Alg44

hetero molecules

A: Alginate biosynthesis protein Alg44

hetero molecules

defined by author&software
27.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alginate biosynthesis protein Alg44

C: Alginate biosynthesis protein Alg44

hetero molecules

defined by author&software
27.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.253, 57.253, 178.350
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-317- HOH

#1: Protein	Alginate biosynthesis protein Alg44 Mass: 12486.075 Da / Num. of mol.: 3 / Fragment: PilZ domain / Mutation: L69(MSE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: alg44, PA3542 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HY69
#2: Chemical	ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate Mass: 690.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₄P₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H₂O
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: 2.25 Å³/Da / Density % sol: 45.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.9 Details: 24% PEG 3350, 0.1M citric acid, pH 2.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2012
Radiation	Monochromator: Si (111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 60645 / % possible obs: 100 %
Reflection shell	Resolution: 1.8→1.86 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
RESOLVE		model building
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→49.583 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 26.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2223	3682	6.07 %	Random
R_work	0.1871	-	-	-
obs	0.1893	60645	99.89 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→49.583 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2431	0	284	168	2883

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2794
X-RAY DIFFRACTION	f_angle_d	1.135	3845
X-RAY DIFFRACTION	f_dihedral_angle_d	14.92	980
X-RAY DIFFRACTION	f_chiral_restr	0.067	422
X-RAY DIFFRACTION	f_plane_restr	0.004	454

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 (%)
1.7991-1.8228	0.3497	142	0.2724	2194	X-RAY DIFFRACTION	100
1.8228-1.8477	0.3132	148	0.2515	2209	X-RAY DIFFRACTION	100
1.8477-1.8741	0.3445	136	0.2457	2175	X-RAY DIFFRACTION	99
1.8741-1.9021	0.2803	140	0.227	2181	X-RAY DIFFRACTION	100
1.9021-1.9318	0.2717	150	0.2224	2170	X-RAY DIFFRACTION	100
1.9318-1.9635	0.2453	142	0.2125	2204	X-RAY DIFFRACTION	100
1.9635-1.9974	0.3399	133	0.2082	2167	X-RAY DIFFRACTION	100
1.9974-2.0337	0.271	140	0.2019	2194	X-RAY DIFFRACTION	100
2.0337-2.0728	0.2867	138	0.2022	2192	X-RAY DIFFRACTION	100
2.0728-2.1151	0.2643	146	0.2099	2228	X-RAY DIFFRACTION	100
2.1151-2.1611	0.2416	129	0.1998	2144	X-RAY DIFFRACTION	100
2.1611-2.2114	0.2876	142	0.2088	2235	X-RAY DIFFRACTION	100
2.2114-2.2667	0.229	148	0.208	2172	X-RAY DIFFRACTION	100
2.2667-2.328	0.241	136	0.1988	2163	X-RAY DIFFRACTION	100
2.328-2.3965	0.2929	156	0.1973	2206	X-RAY DIFFRACTION	100
2.3965-2.4738	0.2413	140	0.1995	2212	X-RAY DIFFRACTION	100
2.4738-2.5622	0.2874	132	0.2114	2156	X-RAY DIFFRACTION	100
2.5622-2.6648	0.2992	140	0.2148	2208	X-RAY DIFFRACTION	100
2.6648-2.7861	0.2184	140	0.2149	2212	X-RAY DIFFRACTION	100
2.7861-2.9329	0.2319	144	0.1935	2176	X-RAY DIFFRACTION	100
2.9329-3.1167	0.2619	133	0.1975	2206	X-RAY DIFFRACTION	100
3.1167-3.3573	0.2272	143	0.1704	2213	X-RAY DIFFRACTION	100
3.3573-3.695	0.186	160	0.1669	2166	X-RAY DIFFRACTION	100
3.695-4.2295	0.182	154	0.1629	2156	X-RAY DIFFRACTION	100
4.2295-5.3277	0.1566	137	0.1541	2216	X-RAY DIFFRACTION	100
5.3277-49.6014	0.1933	133	0.1854	2208	X-RAY DIFFRACTION	100

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	4.1171	1.4172	0.2798	3.7673	-0.8274	3.2944	-0.0907	-0.3321	0.398	-0.2419	0.1977	0.1336	0.1224	-0.6873	-0.1594	0.2038	0.0062	0.0127	0.29	0.0068	0.1134	56.2774	4.5061	75.4937
2	8.2293	-0.1509	-1.0408	5.0473	1.4141	1.5842	0.25	-0.0153	0.2653	-0.4347	-0.153	0.0652	-0.0742	-0.6718	-0.1224	0.2482	0.0676	-0.0084	0.3991	0.017	0.1526	53.41	5.8423	74.7819
3	1.801	0.918	0.3228	2.8087	-2.8694	5.7456	-0.2028	0.2954	0.3149	-0.4106	0.4723	0.1729	0.407	-1.1221	-0.2556	0.3146	-0.0538	-0.0251	0.5765	0.0799	0.2883	51.5244	1.1005	74.8734
4	1.8793	-0.2268	0.5439	2.6074	-2.2407	7.2298	-0.0787	0.1654	0.0078	-0.3907	0.0519	0.0843	0.9734	-0.228	0.006	0.2053	-0.0729	0.0056	0.4358	0.0234	0.1787	55.2751	-1.0859	73.3987
5	5.6874	-0.3536	-2.691	6.38	1.1771	8.2219	-0.376	-1.1802	0.0889	0.8284	0.5636	0.3734	0.2016	-0.4683	0.0247	0.2533	0.0841	0.0099	0.5436	-0.0001	0.1661	55.878	1.7974	80.8945
6	7.8953	-0.0488	0.4044	3.1535	-4.6229	6.7342	-0.2779	-0.0515	0.4354	0.2763	0.147	-0.5249	-0.4448	0.07	0.0572	0.2556	0.0208	0.0119	0.2793	-0.0348	0.195	66.1267	3.1307	65.0762
7	2.4849	0.6803	3.3198	5.186	-0.2527	9.6176	0.149	0.4378	1.1875	-0.1843	-0.4105	0.4465	-0.3797	-0.535	0.3653	0.2827	0.0547	-0.0221	0.3506	-0.0514	0.4278	25.6793	25.3317	58.7922
8	4.1171	-5.3214	-3.443	7.2174	5.2882	4.7423	-0.0717	0.3186	0.2435	0.5531	-0.1509	-0.5143	0.5836	0.9035	0.2007	0.4069	0.1112	0.0269	0.5492	0.0666	0.212	40.6616	8.6202	57.3491
9	8.0016	-4.6783	-1.6577	4.3319	2.9142	5.1692	-0.1064	-0.1266	0.3974	0.4334	0.019	-0.3496	0.0187	0.4597	0.0799	0.264	-0.0999	-0.0358	0.365	0.0555	0.2295	35.006	18.3703	58.4263
10	2.3635	1.7749	3.0517	2.8713	2.6093	6.5982	-0.0024	0.1593	0.2397	0.3444	-0.0234	-0.1695	0.5868	0.4241	0.0111	0.3686	0.0411	0.0235	0.3856	-0.0109	0.3001	35.0878	13.6472	59.1333
11	4.278	-0.4026	2.9674	4.1692	0.5978	6.8431	-0.0745	0.2931	0.2959	0.1785	-0.1283	-0.3531	0.2596	0.1984	0.2818	0.2308	0.0183	0.0486	0.3717	-0.0162	0.2217	32.7741	14.5213	54.5898
12	5.5781	4.5126	-5.598	8.5418	-5.681	5.8885	-0.1094	0.7542	-0.2065	-0.1003	-0.1321	-0.1102	0.387	-0.2753	0.3205	0.3186	-0.0682	0.0141	0.4469	-0.0283	0.2513	27.2278	13.8201	56.2384
13	4.5048	1.7549	-2.164	3.3401	-1.3931	3.7544	-0.5019	0.3016	0.3293	0.3886	0.6819	0.3743	-0.6826	-0.2109	-0.1477	0.3958	0.0297	-0.0317	0.3731	-0.0035	0.2577	22.2879	21.0431	68.9277
14	2.7085	-1.1329	0.2475	2.2398	-0.6426	7.9623	0.1196	0.3907	-0.3523	-0.5221	-0.3885	1.2195	-0.403	-0.6154	0.2143	0.2356	0.0175	-0.061	0.3759	-0.0967	0.4643	19.0455	14.1449	89.7903
15	4.6789	-2.4177	2.4868	1.5857	-2.0395	2.9813	0.5632	0.6864	-0.5231	-0.1839	-0.0251	-0.4077	0.487	1.1578	-0.0311	0.0195	0.2578	-0.0896	0.8327	-0.1603	0.3065	36.916	9.68	87.7802
16	1.5668	0.7264	1.2793	0.3373	0.5925	1.0445	-0.629	-0.3528	-0.4972	0.0677	0.0938	-0.2393	0.8133	0.6532	-0.1905	0.3638	0.3251	0.1054	1.3068	-0.2561	0.3641	45.5213	10.9635	96.4579
17	4.3665	1.3965	1.2891	5.1569	-1.0437	2.4517	-0.1736	0.1982	-0.6528	0.0738	0.3599	0.2721	0.2305	0.5353	-0.1757	0.3093	0.13	-0.0189	0.4174	-0.0696	0.2914	29.6275	9.8441	90.5426
18	1.9835	0.9782	1.6098	1.3088	3.1274	7.7436	-0.0553	0.367	-0.3389	-0.0441	0.3338	-0.0753	0.4796	1.4364	-0.2705	0.3374	0.0987	0.0004	0.5667	-0.0666	0.3038	33.8859	12.4199	90.0792
19	2.7474	1.1879	1.1773	2.9727	4.2918	8.064	-0.0437	0.2666	-0.1567	-0.1374	0.0696	0.001	-0.1163	0.8427	0.0561	0.1678	0.0653	-0.0071	0.3575	-0.0036	0.2065	30.7745	15.5714	92.2934
20	4.2907	3.6185	3.0988	8.3705	1.2414	5.8698	-0.1522	0.3069	0.1026	0.0947	-0.1097	0.0347	-0.3576	0.2457	0.1966	0.2343	0.031	-0.0383	0.3476	-0.0217	0.2207	20.5964	17.1398	79.2787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 14:36)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 37:53)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 54:75)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 76:89)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 90:104)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 105:122)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 15:25)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 26:36)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 37:53)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 54:77)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 78:94)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 95:104)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 105:121)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 16:25)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 26:31)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 32:36)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 37:53)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 54:75)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 76:104)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 105:122)

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