PDB-4o8v: O-Acetyltransferase Domain of Pseudomonas putida AlgJ

ID or keywords:

Entry

Database: PDB / ID: 4o8v

Title

O-Acetyltransferase Domain of Pseudomonas putida AlgJ

Components

Alginate biosynthesis protein AlgJ

Keywords

TRANSFERASE / SGNH Hydrolase-like

Function / homology

Alginate O-acetyltranferase AlgJ / AlgX/AlgJ, SGNH hydrolase-like domain / SGNH hydrolase-like domain, acetyltransferase AlgX / alginic acid biosynthetic process / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / periplasmic space / plasma membrane / Probable alginate O-acetylase AlgJ

Function and homology information

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.815 Å

Authors

Ricer, T. / Little, D.J. / Whitney, J.C. / Robinson, H. / Howell, P.L.

Citation

Journal: Plos Pathog. / Year: 2014
Title: P. aeruginosa SGNH Hydrolase-Like Proteins AlgJ and AlgX Have Similar Topology but Separate and Distinct Roles in Alginate Acetylation.
Authors: Baker, P. / Ricer, T. / Moynihan, P.J. / Kitova, E.N. / Walvoort, M.T. / Little, D.J. / Whitney, J.C. / Dawson, K. / Weadge, J.T. / Robinson, H. / Ohman, D.E. / Codee, J.D. / Klassen, J.S. / ...

History

Deposition	Dec 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4o8v.cif.gz	240.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4o8v.ent.gz	195.7 KB	Display	PDB format
PDBx/mmJSON format	4o8v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4o8v_validation.pdf.gz	430.3 KB	Display	wwPDB validaton report
Full document	4o8v_full_validation.pdf.gz	433 KB	Display
Data in XML	4o8v_validation.xml.gz	26.7 KB	Display
Data in CIF	4o8v_validation.cif.gz	36.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o8/4o8v ftp://data.pdbj.org/pub/pdb/validation_reports/o8/4o8v	HTTPS FTP

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Related structure data

Similar structure data	6l46-d 3r8u-d 6alw-2 3qtx-d 1xbc-d 6z9c-d 1p8h-d 1u59-d 3qtu-d 5fm3-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

Deposited unit

A: Alginate biosynthesis protein AlgJ

B: Alginate biosynthesis protein AlgJ

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

1

A: Alginate biosynthesis protein AlgJ

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

2

B: Alginate biosynthesis protein AlgJ

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

Unit cell

Length a, b, c (Å)	192.493, 33.998, 82.915
Angle α, β, γ (deg.)	90.00, 91.93, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Alginate biosynthesis protein AlgJ Mass: 34565.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: algJ, PP_1279 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus(DE3)-RP / References: UniProt: Q88ND3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 271 / 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: 1.96 Å³/Da / Density % sol: 37.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris pH 5.5, 25% (w/v) PEG 3350, 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: Apr 17, 2012
Radiation	Monochromator: 111 sagittal bend cryo cooled double crystal monochrometer Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.815→50 Å / Num. obs: 48465 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / R_merge(I) obs: 0.101
Reflection shell	Resolution: 1.815→1.9 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.454 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.815→48.096 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 23.92 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2155	1975	4.19 %	Random
R_work	0.1762	-	-	-
obs	0.1778	47176	95.46 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.815→48.096 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4317	0	0	271	4588

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4604
X-RAY DIFFRACTION	f_angle_d	1.096	6297
X-RAY DIFFRACTION	f_dihedral_angle_d	14.553	1706
X-RAY DIFFRACTION	f_chiral_restr	0.048	673
X-RAY DIFFRACTION	f_plane_restr	0.006	858

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 (%)
1.815-1.8602	0.2746	83	0.2334	2122	X-RAY DIFFRACTION	63
1.8602-1.9105	0.2613	142	0.2227	3142	X-RAY DIFFRACTION	93
1.9105-1.9668	0.2642	136	0.2132	3139	X-RAY DIFFRACTION	95
1.9668-2.0302	0.2693	140	0.2034	3237	X-RAY DIFFRACTION	96
2.0302-2.1028	0.2401	150	0.1876	3256	X-RAY DIFFRACTION	97
2.1028-2.187	0.2517	140	0.1861	3258	X-RAY DIFFRACTION	98
2.187-2.2865	0.256	139	0.1874	3318	X-RAY DIFFRACTION	98
2.2865-2.4071	0.2192	144	0.1781	3282	X-RAY DIFFRACTION	98
2.4071-2.5579	0.2814	144	0.1885	3326	X-RAY DIFFRACTION	98
2.5579-2.7553	0.2433	145	0.1901	3341	X-RAY DIFFRACTION	99
2.7553-3.0326	0.2247	154	0.1874	3364	X-RAY DIFFRACTION	100
3.0326-3.4713	0.2219	151	0.1827	3424	X-RAY DIFFRACTION	100
3.4713-4.373	0.1634	150	0.1501	3427	X-RAY DIFFRACTION	100
4.373-48.1129	0.1924	157	0.1605	3565	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	4.8009	-1.0206	5.1505	0.9671	-1.5413	6.0733	-0.1314	0.2503	0.3701	-0.0592	-0.1581	-0.1347	-0.3794	0.3076	0.2929	0.2981	0.016	0.0399	0.1962	-0.0149	0.218	72.1837	20.8876	-16.7812
2	2.7223	-0.6604	1.679	1.8631	-0.8978	2.7061	-0.1618	0.1019	0.5295	0.1158	-0.1421	-0.275	-0.4527	0.1418	0.3417	0.2668	-0.0057	-0.0092	0.175	-0.0044	0.2713	70.3539	24.5104	-9.8097
3	2.6246	-1.2833	2.0128	1.4806	-1.086	2.8152	-0.1603	-0.3083	0.3853	0.1548	-0.0194	-0.0466	-0.3949	-0.1719	0.1243	0.2669	-0.0117	0.0045	0.2289	-0.0286	0.2357	66.7297	17.9679	-3.0374
4	8.6732	-3.8269	2.9158	2.9577	-1.5004	2.2367	-0.287	-0.9884	0.1542	0.8848	0.2265	-0.1333	-0.1765	-0.3962	-0.0234	0.3383	-0.0127	0.0686	0.3797	-0.0521	0.2761	56.4364	17.0751	-3.2403
5	5.6588	-1.6835	1.688	3.1736	-1.3661	1.8952	0.1819	0.0938	-0.2562	-0.1354	-0.1739	-0.2041	0.1193	0.0452	-0.0968	0.2753	0.0115	0.0035	0.1884	-0.1255	0.0907	68.3534	5.614	-5.2328
6	5.1413	-1.1785	2.6325	0.9318	-0.7106	2.7201	0.2264	-0.2288	-0.307	-0.0965	-0.0386	0.1169	0.2812	-0.2646	-0.1556	0.2516	-0.0365	-0.0108	0.1793	-0.015	0.2301	60.6042	6.0705	-8.5742
7	4.8073	0.3016	-0.9004	1.0502	0.0463	4.9452	-0.1427	0.3323	0.0373	-0.1805	0.0467	0.0142	-0.0453	-0.1223	0.1064	0.2933	0.0176	-0.0056	0.1765	0.0117	0.2164	62.7127	16.2919	-25.9367
8	5.8862	-2.9984	3.2171	6.7189	-6.4976	7.8803	-0.093	0.1393	0.288	0.2464	-0.3313	-0.4845	-0.2605	0.4083	0.4132	0.2111	-0.0126	0.0028	0.2514	-0.0023	0.2548	89.9138	-3.3722	16.1176
9	1.4394	-0.0826	-0.4807	0.8129	-1.1089	5.4044	0.0476	-0.0697	-0.149	0.0231	0.0102	-0.0685	0.411	0.1694	-0.032	0.2728	-0.0389	-0.0208	0.1469	-0.0278	0.2456	79.7448	-12.387	32.0436
10	4.5409	2.0622	-2.8813	4.0527	-3.4406	3.5516	-0.1523	0.0628	-0.3349	-0.3981	-0.145	-0.2041	0.9832	0.4593	0.3296	0.3339	0.0001	-0.0109	0.2266	-0.0323	0.2542	84.6919	-16.7807	23.0865
11	1.4094	0.2265	0.3079	1.8858	-2.1792	5.5603	0.0673	0.1362	-0.3075	-0.1564	-0.0188	-0.0715	0.6634	-0.2545	-0.0134	0.2233	-0.0346	-0.003	0.2547	-0.0255	0.2119	73.8775	-7.6064	18.2489
12	4.1849	1.2717	-1.9665	3.9258	-2.9541	4.8794	-0.1369	0.3787	-0.3257	-0.1722	0.2659	0.1314	0.4519	-0.9067	-0.0989	0.2309	-0.1161	-0.0514	0.3685	-0.0146	0.2926	61.6525	-8.3342	26.785
13	3.3183	-0.4612	-1.357	2.7077	-1.4415	4.7736	0.1221	0.2191	0.3269	0.0251	-0.1745	-0.3203	-0.3425	0.0399	-0.201	0.1413	-0.0507	-0.0553	0.1393	-0.0296	0.2289	74.4733	7.0778	18.4579
14	3.4835	-1.0991	-0.016	3.0536	-1.8706	4.6345	-0.0341	-0.1516	-0.118	0.185	0.0747	-0.0687	-0.2165	-0.0747	0.0249	0.1912	-0.0407	0.0015	0.134	-0.0283	0.1738	71.6958	0.3092	32.0184
15	5.0065	0.4827	-0.5039	1.2595	0.0979	5.2796	0.0836	-0.2708	0.0198	0.1436	0.042	-0.1527	-0.1	0.2829	-0.094	0.2613	-0.0088	-0.0209	0.1152	0.002	0.2153	79.9304	-7.133	40.7881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 79 through 122 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 123 through 164 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 165 through 194 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 195 through 211 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 212 through 249 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 250 through 317 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 318 through 370 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 78 through 100 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 101 through 141 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 142 through 164 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 165 through 194 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 195 through 221 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 222 through 285 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 286 through 328 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 329 through 370 )

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