PDB-3rbh: Structure of alginate export protein AlgE from Pseudomonas aeruginosa

ID or keywords:

Entry

Database: PDB / ID: 3rbh

Title

Structure of alginate export protein AlgE from Pseudomonas aeruginosa

Components

Alginate production protein AlgE

Keywords

TRANSPORT PROTEIN /

Beta-Barrel / Alginate export /

Membrane protein

Function / homology

Porin - #100 / Alginate export domain / Alginate export / alginic acid biosynthetic process /

Porin / cell outer membrane /

Beta Barrel / Mainly Beta / Alginate production protein AlgE

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.301 Å

Authors

Whitney, J.C. / Hay, I.D. / Li, C. / Eckford, P.D. / Robinson, H. / Amaya, M.F. / Wood, L.F. / Ohman, D.E. / Bear, C.E. / Rehm, B.H. / Howell, P.L.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for alginate secretion across the bacterial outer membrane.
Authors: Whitney, J.C. / Hay, I.D. / Li, C. / Eckford, P.D. / Robinson, H. / Amaya, M.F. / Wood, L.F. / Ohman, D.E. / Bear, C.E. / Rehm, B.H. / Lynne Howell, P.

History

Deposition	Mar 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 24, 2011	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rbh.cif.gz	671.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3rbh.ent.gz	572 KB	Display	PDB format
PDBx/mmJSON format	3rbh.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/rb/3rbh ftp://data.pdbj.org/pub/pdb/validation_reports/rb/3rbh	HTTPS FTP

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Related structure data

Similar structure data	4azl-1 3jty-3 4xnk-d 4azl-2 3jty-4 3t24-1 4frt-1 2y0h-d 3oed-1 5k0i-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alginate production protein AlgE

B: Alginate production protein AlgE

C: Alginate production protein AlgE

D: Alginate production protein AlgE

hetero molecules

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

1

A: Alginate production protein AlgE

hetero molecules

defined by software
55.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alginate production protein AlgE

hetero molecules

defined by software
56.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Alginate production protein AlgE

hetero molecules

defined by software
56.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Alginate production protein AlgE

hetero molecules

defined by software
57.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	162.018, 90.696, 160.279
Angle α, β, γ (deg.)	90.00, 107.65, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	Alginate production protein AlgE Mass: 53783.441 Da / Num. of mol.: 4 / Fragment: Residues 33-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: algE, alg76, PA3544 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P18895
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	... ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.61 Å³/Da / Density % sol: 52.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 3350, 0.2M ammonium formate, pH 8.0, 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 315 / Detector: CCD / Date: Feb 3, 2010
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: 2.3→50 Å / Num. obs: 98204 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.3→2.38 Å / % possible all: 99.5

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.301→44.76 Å / SU ML: 0.34 / σ(F): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2591	4583	4.96 %	Random
R_work	0.2212	-	-	-
obs	0.2231	92436	93.98 %	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.74 Å² / k_sol: 0.343 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.9499 Å²	0 Å²	-8.2695 Å²
2-	-	-8.5576 Å²	-0 Å²
3-	-	-	0.6076 Å²

Refinement step

Cycle: LAST / Resolution: 2.301→44.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12898	0	463	612	13973

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	13716
X-RAY DIFFRACTION	f_angle_d	1.086	18463
X-RAY DIFFRACTION	f_dihedral_angle_d	15.702	4835
X-RAY DIFFRACTION	f_chiral_restr	0.076	1854
X-RAY DIFFRACTION	f_plane_restr	0.004	2420

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	B	171	X-RAY DIFFRACTION	POSITIONAL
1	2	A	171	X-RAY DIFFRACTION	POSITIONAL	0.024
1	3	C	171	X-RAY DIFFRACTION	POSITIONAL	0.035
1	4	D	171	X-RAY DIFFRACTION	POSITIONAL	0.033
2	1	B	152	X-RAY DIFFRACTION	POSITIONAL
2	2	A	152	X-RAY DIFFRACTION	POSITIONAL	0.028
2	3	C	149	X-RAY DIFFRACTION	POSITIONAL	0.041
2	4	D	145	X-RAY DIFFRACTION	POSITIONAL	0.043
3	1	B	871	X-RAY DIFFRACTION	POSITIONAL
3	2	A	871	X-RAY DIFFRACTION	POSITIONAL	0.029
3	3	C	868	X-RAY DIFFRACTION	POSITIONAL	0.044
3	4	D	864	X-RAY DIFFRACTION	POSITIONAL	0.043
4	1	B	306	X-RAY DIFFRACTION	POSITIONAL
4	2	A	306	X-RAY DIFFRACTION	POSITIONAL	0.026
4	3	C	306	X-RAY DIFFRACTION	POSITIONAL	0.039
4	4	D	294	X-RAY DIFFRACTION	POSITIONAL	0.038
5	1	B	1399	X-RAY DIFFRACTION	POSITIONAL
5	2	A	1399	X-RAY DIFFRACTION	POSITIONAL	0.027
5	3	C	1397	X-RAY DIFFRACTION	POSITIONAL	0.043
5	4	D	1399	X-RAY DIFFRACTION	POSITIONAL	0.039
6	1	D	8	X-RAY DIFFRACTION	POSITIONAL
6	2	A	8	X-RAY DIFFRACTION	POSITIONAL	0.226
6	3	B	8	X-RAY DIFFRACTION	POSITIONAL	0.226
6	4	C	8	X-RAY DIFFRACTION	POSITIONAL	0.221
7	1	B	100	X-RAY DIFFRACTION	POSITIONAL
7	2	A	100	X-RAY DIFFRACTION	POSITIONAL	0.026
7	3	C	97	X-RAY DIFFRACTION	POSITIONAL	0.038
7	4	D	100	X-RAY DIFFRACTION	POSITIONAL	0.036

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 (%)
2.3006-2.3268	0.3531	121	0.2742	2421	X-RAY DIFFRACTION	76
2.3268-2.3542	0.3108	144	0.258	2583	X-RAY DIFFRACTION	85
2.3542-2.3829	0.2875	143	0.2436	2714	X-RAY DIFFRACTION	87
2.3829-2.413	0.2791	136	0.2348	2680	X-RAY DIFFRACTION	88
2.413-2.4448	0.315	157	0.2432	2772	X-RAY DIFFRACTION	88
2.4448-2.4783	0.3215	134	0.2521	2773	X-RAY DIFFRACTION	90
2.4783-2.5137	0.3481	141	0.253	2828	X-RAY DIFFRACTION	90
2.5137-2.5512	0.2919	128	0.229	2757	X-RAY DIFFRACTION	90
2.5512-2.591	0.2834	157	0.2313	2824	X-RAY DIFFRACTION	91
2.591-2.6335	0.3223	162	0.2163	2858	X-RAY DIFFRACTION	93
2.6335-2.6789	0.2739	158	0.2131	2887	X-RAY DIFFRACTION	94
2.6789-2.7276	0.2732	144	0.2287	2928	X-RAY DIFFRACTION	93
2.7276-2.7801	0.3387	149	0.2274	2863	X-RAY DIFFRACTION	93
2.7801-2.8368	0.2825	169	0.2145	2961	X-RAY DIFFRACTION	95
2.8368-2.8985	0.2753	153	0.2148	2964	X-RAY DIFFRACTION	95
2.8985-2.9659	0.3006	146	0.2159	2960	X-RAY DIFFRACTION	96
2.9659-3.0401	0.2832	162	0.2153	2987	X-RAY DIFFRACTION	97
3.0401-3.1222	0.2504	137	0.2185	3055	X-RAY DIFFRACTION	97
3.1222-3.2141	0.2591	179	0.2176	2981	X-RAY DIFFRACTION	97
3.2141-3.3178	0.244	173	0.2023	3048	X-RAY DIFFRACTION	97
3.3178-3.4363	0.2309	149	0.2049	3048	X-RAY DIFFRACTION	98
3.4363-3.5739	0.2405	150	0.1962	3036	X-RAY DIFFRACTION	97
3.5739-3.7364	0.21	178	0.2082	3051	X-RAY DIFFRACTION	99
3.7364-3.9333	0.2915	160	0.215	3063	X-RAY DIFFRACTION	98
3.9333-4.1796	0.238	158	0.2031	3096	X-RAY DIFFRACTION	99
4.1796-4.502	0.2256	159	0.1948	3104	X-RAY DIFFRACTION	99
4.502-4.9546	0.215	162	0.1893	3115	X-RAY DIFFRACTION	99
4.9546-5.6703	0.2518	172	0.2167	3109	X-RAY DIFFRACTION	100
5.6703-7.1393	0.2468	145	0.2525	3196	X-RAY DIFFRACTION	100
7.1393-44.7684	0.2621	157	0.3025	3191	X-RAY DIFFRACTION	99

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	0.0496	-0.0306	0.0999	0.3075	-0.1918	0.2353	0.0125	0.0484	-0.0422	0.1979	-0.0234	0.0862	-0.1964	0.1508	0.0264	0.1238	-0.0377	0.0193	0.1072	-0.008	0.0796	-32.0158	-14.2762	-55.3517
2	0.0116	-0.01	0.0143	0.0017	-0.0274	0.0156	0.0034	0.0193	0.0439	-0.0997	-0.0004	-0.0027	-0.1715	0.1818	-0.0108	0.1458	-0.0491	0.0731	0.2624	0.0478	0.0419	-36.5053	-7.2586	-71.3317
3	0.0222	-0.0013	0.0148	0.0094	-0.0059	0.0078	-0.004	0.1225	-0.0334	0.0316	0.0791	0.0218	0.0073	0.0798	0.1347	-0.0932	0.1172	0.1825	-0.0282	-0.1643	-0.1572	-40.7517	-22.8406	-69.0681
4	0.1696	-0.0449	0.0615	0.1795	-0.022	0.0282	0.0341	0.1476	-0.1439	-0.0455	0.0223	0.0904	-0.0117	0.0693	0.0042	0.1356	0.0009	-0.039	0.0699	-0.0227	0.0944	-12.8909	21.423	-29.7521
5	0.1374	-0.1081	0.0705	0.2067	-0.0018	0.195	0.0615	0.1273	-0.0594	0.0115	0.0014	-0.0983	0.0703	0.02	-0.0453	0.1364	0.0335	-0.0121	0.1936	-0.0112	0.17	1.0719	14.993	-20.5409
6	0.0051	-0.0052	0.0016	0.0864	-0.0691	0.0324	-0.0249	0.0303	-0.0203	-0.0428	0.0502	0.0902	-0.0658	0.0399	0.0746	0.1191	-0.0753	-0.0276	0.061	-0.0154	0.0713	-1.9807	30.3637	-17.2596
7	0.0142	0.0187	0.0193	0.0299	0.0088	0.0405	-0.1871	0.0716	0.0978	-0.2523	0.1443	0.1383	-0.181	0.0186	-0.0574	0.4754	-0.2241	-0.2363	0.0439	0.0737	0.2899	-21.9765	-22.0903	-25.9773
8	0.4083	0.0763	-0.0831	0.076	-0.0573	0.1349	-0.0465	-0.0957	0.2131	-0.1209	0.1212	0.1204	0.0947	-0.0313	0.0447	0.1173	-0.0065	-0.0307	0.1047	0.0018	0.1655	-13.2641	-14.6689	-10.0138
9	0.1412	-0.0196	0.0775	0.056	0.0195	0.0586	-0.1268	-0.0103	-0.0155	-0.139	0.1114	0.0231	0.0765	-0.0832	0.0005	0.2981	-0.0645	-0.0369	0.0678	0.0545	0.1432	-14.8134	-30.6005	-10.49
10	0.0183	0.0138	-0.0057	0.1615	0.0875	0.0592	0.0447	-0.0611	-0.1264	0.2052	0.1358	-0.1611	0.0906	0.0576	0.2847	0.3342	0.119	-0.1125	0.1399	-0.1455	0.1434	-37.7438	29.4162	-48.0267
11	0.0829	0.0289	-0.0503	0.0139	-0.0089	0.038	-0.096	0.0595	-0.0112	0.0594	0.0621	-0.0266	0.1385	-0.0868	0.009	0.1756	-0.0102	0.0119	0.0821	-0.0134	0.0401	-50.8331	22.1059	-60.5797
12	0.0027	0.012	0.0163	0.0472	-0.0733	0.2146	0.0142	0.0285	0.0368	0.0476	0.1089	-0.0919	0.0497	-0.024	0.1169	0.1472	0.0579	0.0036	0.0872	-0.0486	0.1946	-51.092	38.0184	-59.3996

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 40:229)
2	X-RAY DIFFRACTION	2	(chain A and resid 230:347)
3	X-RAY DIFFRACTION	3	(chain A and resid 348:490)
4	X-RAY DIFFRACTION	4	(chain B and resid 40:233)
5	X-RAY DIFFRACTION	5	(chain B and resid 234:350)
6	X-RAY DIFFRACTION	6	(chain B and resid 351:490)
7	X-RAY DIFFRACTION	7	(chain C and resid 40:208)
8	X-RAY DIFFRACTION	8	(chain C and resid 209:385)
9	X-RAY DIFFRACTION	9	(chain C and resid 386:490)
10	X-RAY DIFFRACTION	10	(chain D and resid 40:208)
11	X-RAY DIFFRACTION	11	(chain D and resid 209:385)
12	X-RAY DIFFRACTION	12	(chain D and resid 386:490)

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