PDB-4wxo: SadC (300-487) from Pseudomonas aeruginosa PAO1

ID or keywords:

Entry

Database: PDB / ID: 4wxo

Title

SadC (300-487) from Pseudomonas aeruginosa PAO1

Components

Uncharacterized protein

Keywords

TRANSFERASE /

GGDEF domain / DGC activity

Function / homology

Function and homology information

positive regulation of single-species biofilm formation / negative regulation of bacterial-type flagellum-dependent cell motility /

diguanylate cyclase activity / bacterial-type flagellum-dependent swarming motility / cell adhesion involved in single-species biofilm formation / single-species biofilm formation /

metal ion binding /

plasma membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.805 Å

Authors

Liu, C. / Liu, S. / Gu, L.

Citation

Journal: To Be Published
Title: Crystal structure of SadC (300-487) from Pseudomonas aeruginosa PAO1
Authors: Liu, C. / Liu, S. / Gu, L.

History

Deposition	Nov 14, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wxo.cif.gz	235 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wx/4wxo ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wxo	HTTPS FTP

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Related structure data

Related structure data	4wxwS 4wxm S: Starting model for refinement
Similar structure data	6a3a-d 6a3e-d 1y7v-3 5dh9-d 4wvf-d 5dif-d 5uwo-d 3gxf-2 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 (1) #133 - Jan 2011 Nitric Oxide Synthase similarity (1) #58 - Oct 2004 G Proteins similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

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

1

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

defined by author&software
145 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.419, 116.449, 88.216
Angle α, β, γ (deg.)	90.00, 110.19, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Uncharacterized protein / SadC Mass: 24110.160 Da / Num. of mol.: 3 / Fragment: UNP residues 300-487 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4332 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HW69
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.25 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 0.1 M Tris-HCl, 1.5 M NH4SO4, 12% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.977 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2011
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. obs: 18174 / % possible obs: 98.8 % / Redundancy: 7.3 % / R_merge(I) obs: 0.08 / Net I/σ(I): 46.74
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.388 / Mean I/σ(I) obs: 7.99 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
SCALEPACK		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4WXW

4wxw

Resolution: 2.805→39.463 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2544	933	5.14 %	Random selection
R_work	0.1999	-	-	-
obs	0.2027	18161	98.2 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.805→39.463 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4332	0	0	13	4345

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4419
X-RAY DIFFRACTION	f_angle_d	1.215	5967
X-RAY DIFFRACTION	f_dihedral_angle_d	20.43	1671
X-RAY DIFFRACTION	f_chiral_restr	0.045	657
X-RAY DIFFRACTION	f_plane_restr	0.004	804

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 (%)
2.8048-2.9526	0.3541	130	0.2427	2343	X-RAY DIFFRACTION	95
2.9526-3.1375	0.2804	129	0.2309	2457	X-RAY DIFFRACTION	98
3.1375-3.3796	0.2531	143	0.2043	2477	X-RAY DIFFRACTION	99
3.3796-3.7195	0.2492	129	0.1987	2481	X-RAY DIFFRACTION	99
3.7195-4.2572	0.2361	131	0.1873	2456	X-RAY DIFFRACTION	99
4.2572-5.3615	0.2363	134	0.1831	2512	X-RAY DIFFRACTION	99
5.3615-39.467	0.2583	137	0.2049	2502	X-RAY DIFFRACTION	98

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	0.3664	0.073	-0.0481	0.0778	0.0915	0.2033	-0.0926	-0.0065	-0.2031	0.2018	-0.3132	0.2817	0.184	-0.4338	-0.0145	0.6965	0.0178	-0.0328	0.5159	-0.0257	0.4412	-21.5976	-10.1431	46.0889
2	0.1929	-0.0476	0.0672	0.6175	-0.6742	0.5582	0.1011	-0.0658	0.3221	-0.3439	-0.1582	0.0391	0.1018	-0.0378	0.031	0.4692	0.0038	-0.062	0.408	0.118	0.4069	-19.2756	-2.2913	18.6649
3	0.4058	-0.1777	0.4005	1.0994	-0.422	0.9603	0.2003	0.1552	-0.0171	-0.6482	-0.3393	-0.1175	0.5501	0.353	-1.8663	0.6742	0.2182	0.0309	0.4876	0.132	0.4048	-18.1023	-3.8653	9.6809
4	3.7411	-3.331	-1.52	3.2543	1.5484	0.7377	0.2722	0.3724	-1.3871	-0.466	0.0951	1.4951	1.076	-1.6051	-0.089	1.8557	0.2729	-0.2149	1.0029	0.2143	0.616	-31.1578	-9.9007	1.3587
5	3.0805	-0.5282	2.4372	2.4466	1.0033	3.0319	0.0064	0.6863	1.0342	0.2573	0.0747	-0.6903	-0.5665	0.3805	-0.026	0.5767	-0.0015	0.0493	0.4234	0.1102	0.6649	-13.3545	8.4775	16.2613
6	0.2593	-0.1085	0.108	0.0038	-0.0248	0.6559	0.2537	-0.2513	1.0042	0.3653	-0.829	-0.2514	-0.8013	-0.9599	-0.0138	0.7868	0.0902	-0.0542	0.5128	0.0709	0.4805	-22.0239	11.0022	16.026
7	0.2855	-0.0806	-0.4039	0.0622	0.1043	0.6048	0.2003	0.4006	0.1936	-0.0448	-0.4688	-1.0431	-0.6023	0.4838	0.7786	0.5317	-0.004	-0.0574	0.441	0.2075	0.6882	-20.3976	10.391	7.2754
8	0.0103	-0.3989	0.1187	1.609	1.2618	1.0545	-0.1194	-0.0172	-0.0925	0.0091	-0.0954	0.0637	0.2048	-0.1272	-0.0136	0.3881	-0.0494	0.0086	0.3312	-0.025	0.3097	-16.235	-35.2217	19.781
9	1.2125	0.4428	-0.4699	2.7211	-0.1667	3.0997	-0.8744	-0.1858	-0.5814	-0.5591	-0.1045	-0.5145	0.9647	0.1839	-1.3309	0.314	-0.429	-0.218	0.4726	-0.5412	-0.1078	-19.9868	-44.2071	10.4362
10	0.9584	-0.3565	-1.5363	0.1821	0.5321	2.434	0.3341	0.105	0.1091	0.7789	-0.1781	-0.3857	-0.4766	-0.0674	0.1021	0.4999	-0.0504	-0.0594	0.4494	-0.0359	0.4221	-7.2325	-19.9167	50.5643
11	0.185	-0.1971	0.2288	0.3651	-0.4209	0.6814	-0.3965	-0.4227	-0.9041	0.2416	-0.1492	-1.6453	-0.1405	1.2573	-0.1983	0.5893	-0.0894	0.1962	0.8508	0.1512	1.1184	10.2662	-18.2825	27.6276
12	0.1344	0.0652	-0.2737	0.5788	0.0739	0.3404	-0.0545	0.0414	-0.1615	-0.5449	0.1263	-1.3676	0.1078	0.6075	0.0079	0.962	-0.1463	0.3116	0.9428	0.0785	0.8963	12.2609	-16.03	19.3058
13	1.1403	-0.1798	1.8412	0.1287	-0.0878	3.0008	-0.9851	0.2127	-0.3888	-0.0408	-0.572	-0.7144	-0.5743	1.1262	-0.8761	0.678	0.363	0.9287	1.0173	0.2728	1.6631	16.7733	-15.1661	20.913
14	0.0011	0.0044	0.0026	0.0119	0.0623	0.2191	0.111	-0.0844	0.0665	0.1224	0.43	-0.3536	-0.2543	0.1717	0.0024	0.7409	0.2001	0.1583	1.8571	0.4434	1.8744	23.3344	-22.1372	29.8983
15	0.1295	-0.0787	0.2599	0.7165	-0.1444	0.5609	0.2617	0.6223	-0.6511	0.0312	0.1749	-0.1931	0.7475	0.3254	0.0394	1.1086	0.0431	0.6193	1.5862	0.0336	1.9702	26.0314	-20.7258	21.4682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 302 through 322 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 323 through 372 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 373 through 430 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 431 through 442 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 443 through 455 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 456 through 472 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 473 through 483 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 302 through 430 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 431 through 483 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 302 through 322 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 323 through 372 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 373 through 429 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 430 through 455 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 456 through 472 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 473 through 483 )

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