PDB-3ecq: Endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumonia...

ID or keywords:

Entry

Database: PDB / ID: 3ecq

Title

Endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae: SeMet structure

Components

Endo-alpha-N-acetylgalactosaminidase

Keywords

HYDROLASE / Distorted (Beta/Alpha)8 (TIM) barrel glycoside hydrolase domain / Cell wall / Peptidoglycan-anchor / Secreted

Function / homology

Function and homology information

endo-alpha-N-acetylgalactosaminidase / endo-alpha-N-acetylgalactosaminidase activity / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.9 Å

Authors

Caines, M.E.C. / Zhu, H. / Vuckovic, M. / Strynadka, N.C.J.

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae: a target for structure-based vaccine design.
Authors: Caines, M.E. / Zhu, H. / Vuckovic, M. / Willis, L.M. / Withers, S.G. / Wakarchuk, W.W. / Strynadka, N.C.

History

Deposition	Sep 1, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 9, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / struct_ref_seq_dif / struct_site 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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	3ecq.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb3ecq.ent.gz	888.4 KB	Display	PDB format
PDBx/mmJSON format	3ecq.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/ec/3ecq ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3ecq	HTTPS FTP

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Related structure data

Similar structure data	6zg3-1 20501 6ygc-d 6acx-3 3ffz-2 4f5c-1 6zg3-2 4w5c-d 4f5c-2 6ac8-3 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	#198 - Jun 2016 Beta-galactosidase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (2) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (2) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Endo-alpha-N-acetylgalactosaminidase

B: Endo-alpha-N-acetylgalactosaminidase

hetero molecules

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

1

A: Endo-alpha-N-acetylgalactosaminidase

hetero molecules

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

2

B: Endo-alpha-N-acetylgalactosaminidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	210.611, 158.209, 112.436
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B
1	5	A
2	5	B
1	6	A
2	6	B
1	7	A
2	7	B

NCS domain segments:

Refine code: 2

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	GLU	GLU	A	A	122 - 307	86 - 271
2	1	1	THR	THR	GLU	GLU	B	B	122 - 307	86 - 271
1	1	2	THR	THR	SER	SER	A	A	330 - 354	294 - 318
2	1	2	THR	THR	SER	SER	B	B	330 - 354	294 - 318
1	2	2	LEU	LEU	GLN	GLN	A	A	360 - 601	324 - 565
2	2	2	LEU	LEU	GLN	GLN	B	B	360 - 601	324 - 565
1	1	3	GLY	GLY	GLU	GLU	A	A	602 - 655	566 - 619
2	1	3	GLY	GLY	GLU	GLU	B	B	602 - 655	566 - 619
1	2	3	HIS	HIS	SER	SER	A	A	661 - 721	625 - 685
2	2	3	HIS	HIS	SER	SER	B	B	661 - 721	625 - 685
1	3	3	GLY	GLY	GLU	GLU	A	A	730 - 796	694 - 760
2	3	3	GLY	GLY	GLU	GLU	B	B	730 - 796	694 - 760
1	4	3	GLY	GLY	HIS	HIS	A	A	800 - 808	764 - 772
2	4	3	GLY	GLY	HIS	HIS	B	B	800 - 808	764 - 772
1	5	3	GLY	GLY	TYR	TYR	A	A	818 - 859	782 - 823
2	5	3	GLY	GLY	TYR	TYR	B	B	818 - 859	782 - 823
1	6	3	ASN	ASN	PHE	PHE	A	A	874 - 893	838 - 857
2	6	3	ASN	ASN	PHE	PHE	B	B	874 - 893	838 - 857
1	1	4	THR	THR	THR	THR	A	A	894 - 907	858 - 871
2	1	4	THR	THR	THR	THR	B	B	894 - 907	858 - 871
1	2	4	LYS	LYS	ARG	ARG	A	A	914 - 1043	878 - 1007
2	2	4	LYS	LYS	ARG	ARG	B	B	914 - 1043	878 - 1007
1	1	5	HIS	HIS	GLU	GLU	A	A	1058 - 1213	1022 - 1177
2	1	5	HIS	HIS	GLU	GLU	B	B	1058 - 1213	1022 - 1177
1	1	6	ASN	ASN	SER	SER	A	A	1214 - 1339	1178 - 1303
2	1	6	ASN	ASN	SER	SER	B	B	1214 - 1339	1178 - 1303
1	2	6	LEU	LEU	GLU	GLU	A	A	1349 - 1417	1313 - 1381
2	2	6	LEU	LEU	GLU	GLU	B	B	1349 - 1417	1313 - 1381
1	1	7	THR	THR	LEU	LEU	A	A	1421 - 1434	1385 - 1398
2	1	7	THR	THR	LEU	LEU	B	B	1421 - 1434	1385 - 1398
1	2	7	LYS	LYS	ILE	ILE	A	A	1451 - 1476	1415 - 1440
2	2	7	LYS	LYS	ILE	ILE	B	B	1451 - 1476	1415 - 1440

NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	Endo-alpha-N-acetylgalactosaminidase / protein spr0328 Mass: 171609.422 Da / Num. of mol.: 2 / Fragment: UNP residues 40-1567 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr0328 / Plasmid: pCWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8DR60, endo-alpha-N-acetylgalactosaminidase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.73 Å³/Da / Density % sol: 54.93 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 29% (w/v) PEG MME 2000, 0.2 M lithium citrate, 0.1 M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2006
Radiation	Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.9→112.509 Å / Num. obs: 83445 / % possible obs: 99.4 % / Redundancy: 6.8 % / B_iso Wilson estimate: 71.87 Å² / R_merge(I) obs: 0.11 / R_sym value: 0.11 / Net I/σ(I): 6.13
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.592 / Mean I/σ(I) obs: 2.4 / Num. measured all: 74051 / Num. unique all: 11781 / R_sym value: 0.592 / % possible all: 97.4

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.17	data scaling
SHARP		phasing
SOLOMON		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.9→112.509 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.907 / WR_factor R_free: 0.225 / WR_factor R_work: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU B: 30.846 / SU ML: 0.268 / SU R Cruickshank DPI: 0.313 / SU R_free: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.36
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ATOM RECORDS CONTAIN FULL B-FACTORS. THE ANISOU RECORDS RESULT FROM TLS REFINEMENT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.235	4164	5 %	RANDOM
R_work	0.19	-	-	-
obs	0.192	83381	99.37 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 159.15 Å² / B_iso mean: 57.319 Å² / B_iso min: 13.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.99 Å²	0 Å²	0 Å²
2-	-	0.91 Å²	0 Å²
3-	-	-	0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→112.509 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21250	0	18	97	21365

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	21735
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	14463
X-RAY DIFFRACTION	r_angle_refined_deg	1.225	1.926	29429
X-RAY DIFFRACTION	r_angle_other_deg	0.823	3	35240
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.587	5	2679
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.55	25.087	1091
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.777	15	3681
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.645	15	94
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	3139
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	24571
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4427
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	4296
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	14667
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	10506
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	12015
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	555
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.022	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.187	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.125	0.2	15
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.168	0.2	45
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.331	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0.286	1.5	13241
X-RAY DIFFRACTION	r_mcbond_other	0.08	1.5	5536
X-RAY DIFFRACTION	r_mcangle_it	0.625	2	21276
X-RAY DIFFRACTION	r_scbond_it	1.313	3	8901
X-RAY DIFFRACTION	r_scangle_it	2.069	4.5	8152

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	1080	TIGHT POSITIONAL	0.03	0.05
1	1366	MEDIUM POSITIONAL	0.41	0.5
1	1080	TIGHT THERMAL	0.03	0.5
1	1366	MEDIUM THERMAL	0.2	2
2	1578	TIGHT POSITIONAL	0.03	0.05
2	1938	MEDIUM POSITIONAL	0.34	0.5
2	1578	TIGHT THERMAL	0.04	0.5
2	1938	MEDIUM THERMAL	0.28	2
3	1481	TIGHT POSITIONAL	0.04	0.05
3	1927	MEDIUM POSITIONAL	0.33	0.5
3	1481	TIGHT THERMAL	0.05	0.5
3	1927	MEDIUM THERMAL	0.32	2
4	851	TIGHT POSITIONAL	0.03	0.05
4	1119	MEDIUM POSITIONAL	0.32	0.5
4	851	TIGHT THERMAL	0.04	0.5
4	1119	MEDIUM THERMAL	0.26	2
5	923	TIGHT POSITIONAL	0.03	0.05
5	1098	MEDIUM POSITIONAL	0.36	0.5
5	923	TIGHT THERMAL	0.05	0.5
5	1098	MEDIUM THERMAL	0.31	2
6	1143	TIGHT POSITIONAL	0.03	0.05
6	1456	MEDIUM POSITIONAL	0.28	0.5
6	1143	TIGHT THERMAL	0.05	0.5
6	1456	MEDIUM THERMAL	0.31	2
7	239	TIGHT POSITIONAL	0.03	0.05
7	277	MEDIUM POSITIONAL	0.43	0.5
7	239	TIGHT THERMAL	0.03	0.5
7	277	MEDIUM THERMAL	0.2	2

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.403	298	-
R_work	0.351	5616	-
all	-	5914	-
obs	-	5616	96.46 %

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	3.2285	-0.115	-1.1668	6.7896	-1.1069	4.4139	0.1301	0.2391	0.0967	0.1149	0.0326	0.7406	-0.543	-0.3907	-0.1628	0.0717	0.1583	0.1009	-0.0694	-0.0179	-0.0809	54.733	62.3063	13.117
2	1.693	0.3101	-0.3832	1.2298	0.2578	1.3906	0.0709	-0.1837	0.1288	0.0482	0.1041	-0.5938	-0.1656	0.3898	-0.175	-0.2172	-0.0037	-0.027	-0.1376	-0.2635	0.2329	85.9593	41.4699	33.2672
3	0.3338	0.1881	-0.3617	0.9337	0.6113	1.1946	0.062	0.163	0.0279	-0.1556	0.0645	-0.0217	-0.0348	-0.3328	-0.1265	-0.1598	0.0455	0.0558	-0.2092	-0.0939	-0.1054	58.1285	28.2216	19.3914
4	1.4312	0.1047	0.426	1.8535	1.2585	1.6646	0.0681	0.2473	-0.0721	-0.3509	0.131	-0.5428	-0.0705	0.2723	-0.1991	-0.0904	0.0338	0.2284	-0.1148	-0.1632	-0.0382	73.6327	21.9381	-3.4228
5	1.9329	-0.6788	-0.7256	1.7905	0.0104	1.8811	0.0216	0.2941	-0.1049	-0.2257	0.0716	-0.1876	0.2866	-0.0826	-0.0932	-0.1689	-0.1057	0.09	-0.2081	-0.0948	-0.3605	34.8646	10.8131	3.8767
6	1.5321	0.3666	0.1455	1.8526	0.7639	2.077	0.0139	-0.0252	0.2152	0.1069	-0.0193	0.2545	-0.0137	-0.4422	0.0055	-0.2839	-0.011	0.1307	-0.1326	-0.0214	-0.2854	23.9635	29.5415	20.2595
7	12.2032	1.712	1.1614	9.796	10.2931	14.0906	-0.5038	0.1376	1.1371	-0.4793	0.0127	0.3492	-1.0693	-0.9605	0.4911	0.0169	0.0931	0.1267	0.3738	0.0768	0.369	-1.0814	32.0645	20.4993
8	2.6081	1.1827	0.3446	3.4333	0.9031	3.2038	0.0125	0.2775	-0.6135	0.5005	0.115	-0.6857	0.2735	0.4725	-0.1275	0.3712	0.1132	-0.0587	0.3353	-0.1292	0.56	49.4068	23.1371	-43.5874
9	2.2836	0.2269	-0.1171	1.9585	-1.2713	2.0708	-0.0511	0.0574	0.0066	-0.1764	0.0835	0.3615	0.3337	-0.4042	-0.0325	-0.1684	-0.0339	0.0033	-0.1637	-0.0031	-0.1557	21.1809	45.1892	-22.9321
10	0.8699	0.6634	0.105	2.2155	-1.3324	1.6034	0.0436	0.3798	0.0178	-0.2786	-0.0972	-0.4999	0.0492	0.4611	0.0536	-0.1211	0.0548	-0.0055	-0.0816	0.0608	-0.1295	49.7098	58.0662	-36.2605
11	2.5919	1.271	-0.8669	2.1848	-1.3652	2.1782	-0.2196	0.8195	0.5824	-0.6476	0.406	0.4572	0.3461	-0.5118	-0.1864	0.1077	-0.0343	-0.1591	0.2622	0.2551	-0.1114	34.4872	65.6795	-58.7807
12	1.691	-0.9035	0.3902	1.6015	0.4254	1.6509	0.177	0.3904	-0.0932	-0.25	0.1939	0.1606	-0.3791	0.0594	-0.3709	-0.1119	-0.0455	0.0817	-0.1649	-0.0149	-0.2604	73.795	74.9191	-51.1443
13	2.2754	0.5348	-0.2841	1.4421	-0.6129	2.3926	0.3007	0.0389	-0.6923	0.0605	0.0765	-0.2889	0.1358	0.2629	-0.3772	-0.2831	-0.0281	-0.1734	-0.174	-0.1051	0.0706	83.6644	55.0316	-35.5462
14	6.7846	-0.601	-0.8573	7.7689	-2.2425	5.4419	0.0706	0.561	-1.0351	-0.6792	-0.1737	0.4653	0.7789	0.2558	0.1031	0.0535	0.1289	-0.2203	0.547	-0.346	0.3985	106.5463	45.9045	-38.6047

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	119 - 307	83 - 271
2	X-RAY DIFFRACTION	2	A	A	319 - 601	283 - 565
3	X-RAY DIFFRACTION	3	A	A	602 - 893	566 - 857
4	X-RAY DIFFRACTION	4	A	A	894 - 1057	858 - 1021
5	X-RAY DIFFRACTION	5	A	A	1058 - 1213	1022 - 1177
6	X-RAY DIFFRACTION	6	A	A	1214 - 1417	1178 - 1381
7	X-RAY DIFFRACTION	7	A	A	1418 - 1476	1382 - 1440
8	X-RAY DIFFRACTION	8	B	B	122 - 307	86 - 271
9	X-RAY DIFFRACTION	9	B	B	318 - 601	282 - 565
10	X-RAY DIFFRACTION	10	B	B	602 - 893	566 - 857
11	X-RAY DIFFRACTION	11	B	B	894 - 1057	858 - 1021
12	X-RAY DIFFRACTION	12	B	B	1058 - 1213	1022 - 1177
13	X-RAY DIFFRACTION	13	B	B	1214 - 1417	1178 - 1381
14	X-RAY DIFFRACTION	14	B	B	1418 - 1481	1382 - 1445

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