PDB-4rt1: Structure of the Alg44 PilZ domain (R95A mutant) from Pseudomonas...

ID or keywords:

Entry

Database: PDB / ID: 4rt1

Title

Structure of the Alg44 PilZ domain (R95A mutant) 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 /

MOLECULAR REPLACEMENT / Resolution: 1.7 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	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	4rt1.cif.gz	157 KB	Display	PDBx/mmCIF format
PDB format	pdb4rt1.ent.gz	126 KB	Display	PDB format
PDBx/mmJSON format	4rt1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4rt1_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4rt1_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4rt1_validation.xml.gz	20.1 KB	Display
Data in CIF	4rt1_validation.cif.gz	28.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rt/4rt1 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/4rt1	HTTPS FTP

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Related structure data

Related structure data	4rt0SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2msb-d 4rt0-1 1mel-1 3grv-d 1jto-2 6baq-1 2o2t-d 2w7a-d 2yj4-1 3lqi-1 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

39.2 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
26.2 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
26.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.075, 106.075, 122.314
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-393- HOH
2	1	C-301- HOH
3	1	C-370- HOH

#1: Protein	Alginate biosynthesis protein Alg44 Mass: 12353.064 Da / Num. of mol.: 3 / Fragment: PilZ domain / Mutation: L69M, R95A 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.: 3 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₄P₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 400, 0.2M NaCl, 0.1M HEPES, pH 7.5, 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: 1.075 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: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. obs: 84860 / % possible obs: 100 %
Reflection shell	Resolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Entry 4RT0

4rt0

Resolution: 1.7→48.66 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 18.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2012	3766	4.44 %	Random
R_work	0.1654	-	-	-
obs	0.167	84860	99.69 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→48.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2454	0	140	377	2971

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2827
X-RAY DIFFRACTION	f_angle_d	1.374	3888
X-RAY DIFFRACTION	f_dihedral_angle_d	14.529	1043
X-RAY DIFFRACTION	f_chiral_restr	0.094	428
X-RAY DIFFRACTION	f_plane_restr	0.006	494

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 (%)
1.6975-1.719	0.2103	126	0.1829	2801	X-RAY DIFFRACTION	93
1.719-1.7416	0.2212	138	0.1857	3009	X-RAY DIFFRACTION	100
1.7416-1.7655	0.2377	139	0.1765	3020	X-RAY DIFFRACTION	100
1.7655-1.7907	0.2368	143	0.1833	2995	X-RAY DIFFRACTION	100
1.7907-1.8175	0.2018	143	0.1788	3000	X-RAY DIFFRACTION	100
1.8175-1.8459	0.2292	137	0.1662	3002	X-RAY DIFFRACTION	100
1.8459-1.8761	0.2315	140	0.1716	3040	X-RAY DIFFRACTION	100
1.8761-1.9085	0.2112	140	0.1612	3008	X-RAY DIFFRACTION	100
1.9085-1.9432	0.1773	140	0.1517	2994	X-RAY DIFFRACTION	100
1.9432-1.9805	0.1825	137	0.1568	3010	X-RAY DIFFRACTION	100
1.9805-2.021	0.1977	140	0.1567	3013	X-RAY DIFFRACTION	100
2.021-2.0649	0.216	141	0.162	3015	X-RAY DIFFRACTION	100
2.0649-2.113	0.1969	136	0.1519	3009	X-RAY DIFFRACTION	100
2.113-2.1658	0.1952	134	0.1481	3012	X-RAY DIFFRACTION	100
2.1658-2.2244	0.1645	143	0.1468	2995	X-RAY DIFFRACTION	100
2.2244-2.2898	0.1984	140	0.1588	3020	X-RAY DIFFRACTION	100
2.2898-2.3637	0.1779	139	0.1544	3005	X-RAY DIFFRACTION	100
2.3637-2.4482	0.1964	139	0.1637	3043	X-RAY DIFFRACTION	100
2.4482-2.5462	0.1916	141	0.1698	2988	X-RAY DIFFRACTION	100
2.5462-2.6621	0.2072	143	0.1793	3045	X-RAY DIFFRACTION	100
2.6621-2.8024	0.2262	138	0.1746	2993	X-RAY DIFFRACTION	100
2.8024-2.978	0.2273	143	0.1787	2992	X-RAY DIFFRACTION	100
2.978-3.2079	0.2394	143	0.178	3030	X-RAY DIFFRACTION	100
3.2079-3.5306	0.1658	140	0.1619	3006	X-RAY DIFFRACTION	100
3.5306-4.0413	0.1694	144	0.1509	2999	X-RAY DIFFRACTION	100
4.0413-5.0907	0.202	138	0.1454	3031	X-RAY DIFFRACTION	100
5.0907-48.6798	0.2334	141	0.2006	3019	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	4.5894	-1.9879	0.0184	5.3503	-1.554	2.7796	-0.0774	0.0212	0.1027	-0.0074	0.0409	-0.0532	-0.0421	-0.0513	0.0347	0.0441	-0.0706	-0.0032	0.1348	-0.0521	0.0864	24.4251	-31.661	138.2826
2	2.4142	0.7089	-0.1871	1.265	-0.448	2.8776	-0.0288	0.2704	0.0655	-0.0677	0.0681	0.0143	-0.1204	-0.1331	-0.0168	0.0836	-0.0216	0.0032	0.153	-0.0032	0.1346	21.3144	-29.6737	138.1872
3	8.4583	0.9366	-0.6563	6.1864	-0.086	4.5231	-0.0884	0.3416	-0.0478	-0.2938	-0.13	-0.4176	0.1023	0.218	0.1867	0.1848	-0.0525	0.0153	0.3072	-0.0247	0.1708	25.2919	-40.0314	127.5948
4	7.4061	-1.2261	1.3925	5.777	-1.7465	6.0488	-0.0106	0.0963	-0.0789	0.0024	0.0225	-0.3752	0.1583	0.1796	0.0054	0.1218	-0.0209	-0.0082	0.0695	-0.0341	0.1555	48.4311	-9.5271	137.6145
5	8.5807	0.3964	-1.53	4.5712	-0.6187	5.2112	0.1159	-0.1038	0.2834	0.1475	0.2161	0.7199	-0.0203	-1.1356	-0.0935	0.1476	-0.0188	-0.0188	0.2504	0.0253	0.2173	26.8722	-6.4449	138.2726
6	2.1543	-0.0111	-1.0666	2.0233	0.0547	3.2872	-0.0055	0.0863	0.1677	0.0371	0.044	0.1648	-0.1301	-0.274	-0.0461	0.1018	-0.0055	-0.0179	0.0826	-0.0096	0.1218	35.0931	-5.5764	141.4361
7	1.4967	0.6426	-2.4662	1.7287	-2.2426	8.779	0.1367	0.1771	0.1873	-0.2521	0.0896	-0.0411	-0.7058	0.2236	-0.1942	0.3443	-0.0793	0.0237	0.1493	-0.0164	0.235	33.156	-8.7659	129.6927
8	0.808	0.2251	0.4232	1.7582	-0.5251	1.8805	-0.0857	0.1571	0.0554	-0.1746	0.129	0.0186	0.0084	0.0343	-0.0244	0.1347	-0.0379	0.0136	0.0927	0.0115	0.1101	35.9424	-9.2317	138.8908
9	2.5084	-0.5063	-0.4168	2.2745	1.2426	3.1031	-0.0329	0.5393	-0.0141	-0.4187	0.0402	-0.1788	-0.103	0.0384	-0.0058	0.2377	-0.0446	0.0173	0.1958	-0.0173	0.1712	42.0174	-14.1152	130.9471
10	8.3014	-3.2549	1.7336	6.1949	-1.6246	3.627	0.1861	-0.0715	-0.0768	0.1888	-0.1303	0.1348	0.1441	0.0366	-0.0439	0.2632	-0.0821	-0.0188	0.0709	-0.0425	0.1013	33.9863	-18.1979	106.2581
11	2.6655	0.9361	0.9791	2.6513	-0.3605	2.9044	0.1373	-0.0622	-0.0416	0.2114	0.0083	0.2207	0.084	-0.2064	-0.1193	0.1998	-0.0514	0.0147	0.099	-0.0078	0.1579	30.2016	-18.5155	103.4942
12	0.1259	-0.2902	0.054	2.617	-3.2875	5.0904	0.0057	-0.0829	-0.0931	0.2647	0.1626	0.068	0.3975	-0.4139	-0.2044	0.4152	-0.1343	-0.0103	0.2018	-0.0182	0.2346	30.8925	-14.7228	114.4556
13	0.6516	0.367	-0.422	1.3163	-0.5723	1.5349	0.0205	-0.0242	-0.0018	0.1752	0.0011	0.1066	-0.0086	0.0592	0.0133	0.2149	-0.0575	-0.0047	0.1026	-0.0001	0.1451	33.3046	-15.7384	105.1239
14	2.402	0.0575	0.4233	1.3233	-0.4588	1.7862	-0.0531	-0.3007	-0.1083	0.5814	0.0252	-0.1195	0.0276	0.2336	0.0065	0.3913	-0.0388	-0.0454	0.185	0.0052	0.1826	41.1163	-16.4325	113.3497

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 104 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 105 through 121 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 15 through 25 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 26 through 36 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 37 through 63 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 64 through 75 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 76 through 94 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 95 through 122 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 15 through 36 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 37 through 63 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 64 through 75 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 76 through 94 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 95 through 122 )

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