PDB-2wlg: Crystallographic analysis of the polysialic acid O-acetyltransfer...

ID or keywords:

Entry

Database: PDB / ID: 2wlg

Title

Crystallographic analysis of the polysialic acid O-acetyltransferase OatWY

Components

POLYSIALIC ACID O-ACETYLTRANSFERASE

Keywords

TRANSFERASE / ENZYME / ACETYLTRANSFERASE / LEFT-HANDED BETA HELIX

Function / homology

Function and homology information

polysialic-acid O-acetyltransferase activity / protein homotrimerization / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function

Biological species

NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Lee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.

Citation

Journal: J.Biol.Chem. / Year: 2009
Title: Structural and Kinetic Characterizations of the Polysialic Acid O-Acetyltransferase Oatwy from Neisseria Meningitidis.
Authors: Lee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.

History

Deposition	Jun 23, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 30, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	2wlg.cif.gz	146.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2wlg.ent.gz	115.4 KB	Display	PDB format
PDBx/mmJSON format	2wlg.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/wl/2wlg ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wlg	HTTPS FTP

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Related structure data

Related structure data	2wlcC 2wldC 2wleC 2wlfC C: citing same article (ref.)
Similar structure data	2wld-d 2wlf-d 2wle-d 1ab8-2 4goq-d 5chi-d 1wu8-d 2zwi-d 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	#165 - Sep 2013 Designed Protein Cages similarity (3) #39 - Mar 2003 lac Repressor similarity (3) #49 - Jan 2004 Carbonic Anhydrase similarity (3)

Deposited unit

A: POLYSIALIC ACID O-ACETYLTRANSFERASE

B: POLYSIALIC ACID O-ACETYLTRANSFERASE

C: POLYSIALIC ACID O-ACETYLTRANSFERASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.669, 94.393, 100.874
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	16
Space group name H-M	P222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 6 - 214 / Label seq-ID: 6 - 214

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C

#1: Protein	POLYSIALIC ACID O-ACETYLTRANSFERASE Mass: 23731.191 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LEFT-HANDED BETA HELIX Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria) Strain: 406Y / Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: Q93S40
#2: Chemical	ChemComp-SOP / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE / S-(2-OXOPROPYL)-COENZYME A Mass: 823.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₄H₄₀N₇O₁₇P₃S
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN C, ASN 67 TO ILE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53 % Description: STARTING MODEL WAS MY NAI SOAKING SIRAS STRUCTURE SOLVED BY SHELX-CDE.
Crystal grow	pH: 4.6 Details: 100 MM SODIUM ACETATE, 2.25 M AMMONIUM ACETATE, pH 4.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2008 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.9→40 Å / Num. obs: 59306 / % possible obs: 99 % / Observed criterion σ(I): 7 / Redundancy: 10 % / R_merge(I) obs: 0.05 / Net I/σ(I): 52.8
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 8.9 % / R_merge(I) obs: 0.28 / Mean I/σ(I) obs: 7.2 / % possible all: 95.2

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0066	refinement
HKL		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 1.9→40 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.936 / SU B: 8.47 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23106	2987	5.1 %	RANDOM
R_work	0.19278	-	-	-
obs	0.19473	56022	98.48 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.569 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.35 Å²	0 Å²	0 Å²
2-	-	-1.24 Å²	0 Å²
3-	-	-	-2.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4856	0	168	290	5314

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	5114
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4596
X-RAY DIFFRACTION	r_angle_refined_deg	1.342	1.971	6921
X-RAY DIFFRACTION	r_angle_other_deg	1.044	3	10752
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.133	5	639
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.984	25.714	210
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.409	15	892
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.046	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	801
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5571
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	908
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.513	1.5	3135
X-RAY DIFFRACTION	r_mcbond_other	0.16	1.5	1311
X-RAY DIFFRACTION	r_mcangle_it	0.987	2	5102
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.884	3	1979
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.99	4.5	1813
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 3028 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	loose positional	0.62	5
2	B	loose positional	0.68	5
3	C	loose positional	0.58	5
1	A	loose thermal	2.38	10
2	B	loose thermal	2.71	10
3	C	loose thermal	2.91	10

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.241	189	-
R_work	0.23	3930	-
obs	-	-	94.28 %

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	2.0653	3.4887	3.0446	13.6821	10.6468	10.7393	-0.0574	0.3004	-0.1401	-0.6093	0.0086	0.1218	-0.0266	-0.6357	0.0488	0.4186	-0.0288	-0.041	0.4984	0.0996	0.3471	21.1479	3.4795	-34.8079
2	1.428	0.2484	-0.9276	1.9982	-0.0385	3.9251	-0.0444	0.3519	0.1853	-0.2966	0.0833	0.2278	0.0057	-0.6664	-0.0389	0.1414	-0.0528	-0.0526	0.2553	0.0658	0.1065	27.6276	-1.3864	-36.9375
3	1.7582	0.6065	-0.5112	3.5235	0.4807	4.1327	-0.0801	0.1711	0.1014	-0.1354	0.0324	0.2647	0.1626	-0.4865	0.0477	0.0986	-0.0758	-0.0263	0.1987	0.0286	0.112	29.6126	-5.6735	-31.092
4	5.3124	-7.2233	-10.2967	18.4468	22.5418	30.9817	0.125	-0.1476	0.2578	-0.5046	0.5049	-0.6337	-0.4844	0.8231	-0.63	0.0537	-0.0416	-0.0085	0.1028	0.0543	0.0844	36.6823	-6.1351	-30.1361
5	0.3707	0.0415	-0.6342	1.0792	0.6594	4.178	-0.1223	0.024	-0.054	-0.065	0.0224	-0.0018	0.3708	-0.0972	0.0998	0.0879	-0.0599	0.024	0.102	0.0011	0.0728	32.7155	-13.0302	-19.5539
6	1.6546	0.1673	-1.6249	3.1461	1.504	4.719	-0.2458	-0.0053	-0.2155	-0.0957	0.0678	-0.1428	0.6332	0.0247	0.178	0.1887	-0.0292	0.0581	0.0591	0.0217	0.0567	37.2972	-19.2255	-27.12
7	2.8705	-0.4547	-2.4389	2.4874	1.5681	3.8865	-0.4252	-0.2771	-0.3109	0.0469	0.1878	-0.252	0.8203	0.3578	0.2375	0.2917	0.052	0.1104	0.0929	0.0542	0.1166	41.125	-23.7635	-22.9766
8	5.826	-1.9569	-1.2775	4.6274	-0.6789	5.3288	-0.2977	0.6031	-0.4923	-0.4882	-0.1605	-0.0522	1.0734	0.257	0.4582	0.4866	-0.0449	0.2228	0.1344	-0.031	0.2492	44.6891	-29.6004	-37.4372
9	16.6021	3.4775	-1.4734	3.6302	4.1647	8.6781	0.1206	0.1215	0.5862	0.1535	0.0509	-0.5756	0.2103	0.376	-0.1714	0.5071	-0.047	0.0809	0.2065	0.1769	0.7597	51.7075	-23.0454	-41.0561
10	2.9888	1.6839	-3.048	8.2843	1.1078	4.2851	0.084	0.3086	0.7954	-1.2039	0.4867	0.7131	-0.4305	-0.385	-0.5706	1.1127	0.0061	0.2714	0.647	-0.0249	0.5363	14.2796	-31.2879	-55.253
11	2.834	-0.6087	-1.9854	2.5204	-0.7027	7.1983	0.359	0.011	-0.1403	-0.6431	-0.1344	0.322	1.0395	-1.0409	-0.2246	0.8069	-0.399	-0.0267	0.4288	0.0115	0.1766	10.1916	-37.7251	-46.4373
12	1.9499	-0.5585	0.2723	2.2383	-0.0488	3.6945	0.4662	-0.0839	0.0983	-0.6146	-0.1648	0.0397	0.6419	-0.4398	-0.3014	0.8117	-0.3362	0.0984	0.2508	-0.0312	0.1484	18.1145	-37.5412	-43.1611
13	4.4317	0.4256	-1.9384	1.9269	-1.0924	3.3962	0.0732	-0.0283	-0.1508	-0.5049	0.0437	-0.0862	0.7411	-0.4555	-0.1169	0.7216	-0.3779	0.0749	0.2512	-0.0502	0.1371	20.4905	-39.8539	-34.5083
14	0.9342	0.9231	-0.2858	1.2371	-1.0512	1.9326	-0.0388	-0.0702	-0.1802	-0.3942	0.0294	-0.1854	0.7701	-0.174	0.0093	0.6721	-0.241	0.1867	0.124	-0.0687	0.2224	30.6372	-39.8289	-30.5489
15	3.1057	2.751	-0.1432	6.31	0.7429	5.5834	0.0952	-0.3274	-0.2808	-0.0553	0.0656	-0.8498	1.0474	-0.012	-0.1607	0.692	-0.2994	0.0641	0.2245	-0.0104	0.2653	29.0562	-46.2164	-19.8232
16	7.5718	-0.1566	-1.674	6.8671	-0.1025	3.379	0.0075	-0.0121	-0.2829	-0.2004	0.2268	0.53	0.0821	-0.466	-0.2343	0.6933	-0.4839	0.0214	0.3967	0.05	0.2426	11.5475	-48.8667	-17.8818
17	2.8597	1.6475	-2.7695	6.3046	-1.3894	14.3949	-0.1836	0.0894	-0.2334	-0.2948	0.1382	0.168	0.5326	-0.5954	0.0455	0.7711	-0.5758	-0.0377	0.4653	0.0281	0.3484	8.9022	-56.2804	-19.308
18	16.4156	10.4291	-11.8082	14.9573	-10.5661	13.1777	0.3672	-0.3412	0.6145	-0.2338	-0.2524	0.2881	-0.6604	0.2271	-0.1148	0.3217	-0.2989	0.0123	0.7122	-0.0802	0.5162	-9.7882	-23.1373	-15.3112
19	0.562	1.3013	1.7325	3.1076	4.2154	5.8639	-0.0092	-0.141	0.3677	0.0801	-0.5356	0.6492	0.0313	-0.6348	0.5448	0.1706	-0.2106	0.1103	0.6823	0.0446	0.8285	-4.2041	-16.0439	-10.2687
20	4.9853	5.4717	1.2694	9.1995	2.0491	2.1974	0.0583	0.109	0.2802	0.2556	-0.218	0.4454	0.3804	-0.6248	0.1597	0.1894	-0.2954	0.0025	0.4879	0.0451	0.3238	-1.6784	-19.665	-10.0357
21	2.4226	0.5794	0.1076	1.6276	-0.1651	1.4175	-0.1189	0.0751	0.0894	-0.0588	0.1102	0.2959	0.4461	-0.4802	0.0086	0.2606	-0.2775	0.0254	0.3391	0.0511	0.1797	8.0339	-23.8747	-10.0647
22	2.6261	0.7547	-2.016	9.4021	1.7013	3.6202	0.1438	-0.2418	-0.2468	0.2809	0.0481	0.0842	0.3446	-0.0432	-0.192	0.5572	-0.4116	0.0106	0.3554	0.04	0.2346	12.8066	-48.633	-12.1076
23	2.4738	1.2686	0.2503	2.9901	1.1264	2.4009	0.0029	-0.0292	-0.2465	0.1579	0.0961	-0.1512	0.695	-0.2004	-0.0991	0.2766	-0.1171	0.0094	0.1203	0.0334	0.0847	23.8587	-26.9021	-6.2259
24	1.9903	1.5933	0.2924	4.2989	0.5548	2.5259	-0.0336	-0.1017	0.1682	0.1478	0.0391	0.1008	0.153	-0.1721	-0.0056	0.1117	-0.0386	0.032	0.1922	-0.0004	0.1077	27.6664	-9.3155	-1.2954
25	16.9928	4.6182	-5.3118	20.2279	-7.0344	10.8212	0.3585	-1.5849	-0.1086	1.5093	-0.379	-0.47	-0.2828	0.0529	0.0205	0.2435	-0.0788	0.0946	0.2581	-0.0295	0.1924	24.4757	-11.5729	7.1043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 9
2	X-RAY DIFFRACTION	2	A	10 - 49
3	X-RAY DIFFRACTION	3	A	50 - 75
4	X-RAY DIFFRACTION	4	A	76 - 85
5	X-RAY DIFFRACTION	5	A	86 - 134
6	X-RAY DIFFRACTION	6	A	135 - 152
7	X-RAY DIFFRACTION	7	A	153 - 184
8	X-RAY DIFFRACTION	8	A	185 - 208
9	X-RAY DIFFRACTION	9	A	209 - 215
10	X-RAY DIFFRACTION	10	B	6 - 11
11	X-RAY DIFFRACTION	11	B	12 - 48
12	X-RAY DIFFRACTION	12	B	49 - 80
13	X-RAY DIFFRACTION	13	B	81 - 119
14	X-RAY DIFFRACTION	14	B	120 - 170
15	X-RAY DIFFRACTION	15	B	171 - 190
16	X-RAY DIFFRACTION	16	B	191 - 201
17	X-RAY DIFFRACTION	17	B	202 - 214
18	X-RAY DIFFRACTION	18	C	6 - 10
19	X-RAY DIFFRACTION	19	C	11 - 26
20	X-RAY DIFFRACTION	20	C	27 - 45
21	X-RAY DIFFRACTION	21	C	46 - 118
22	X-RAY DIFFRACTION	22	C	119 - 135
23	X-RAY DIFFRACTION	23	C	136 - 189
24	X-RAY DIFFRACTION	24	C	190 - 209
25	X-RAY DIFFRACTION	25	C	210 - 215

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