PDB-9awt: Structure of the A type blood alpha-D-galactosamine galactosamini...

ID or keywords:

Entry

Database: PDB / ID: 9awt

Title

Structure of the A type blood alpha-D-galactosamine galactosaminidase from Flavonifractor plautii in complex with GalN-pNP

Components

A type blood alpha-D-galactosamine galactosaminidase

Keywords

SUGAR BINDING PROTEIN / galactosaminidase

Function / homology

Function and homology information

alpha-galactosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
Similarity search - Function

Biological species

Flavonifractor plautii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Worrall, L.J. / Strynadka, N.C.J.

Funding support

Canada, 1items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Cobalt as a Cofactor for alpha-Galactosaminidase-Catalyzed Cleavage of Blood Group Antigens
Authors: Tian, Y. / Worrall, L.J. / Sim, L. / Liu, F. / Nasseri, S.A. / Rahfeld, P. / Mu, W. / Kizhakkedathu, J.N. / Strynadka, N.C.J. / Withers, S.G.

History

Deposition	Mar 5, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9awt.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb9awt.ent.gz		Display	PDB format
PDBx/mmJSON format	9awt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9awt_validation.pdf.gz	5.5 MB	Display	wwPDB validaton report
Full document	9awt_full_validation.pdf.gz	5.5 MB	Display
Data in XML	9awt_validation.xml.gz	148.8 KB	Display
Data in CIF	9awt_validation.cif.gz	203.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aw/9awt ftp://data.pdbj.org/pub/pdb/validation_reports/aw/9awt	HTTPS FTP

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Related structure data

Related structure data	9ay8C 9ayuC C: citing same article (ref.)
Similar structure data	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	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: A type blood alpha-D-galactosamine galactosaminidase

B: A type blood alpha-D-galactosamine galactosaminidase

C: A type blood alpha-D-galactosamine galactosaminidase

D: A type blood alpha-D-galactosamine galactosaminidase

E: A type blood alpha-D-galactosamine galactosaminidase

hetero molecules

371 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: A type blood alpha-D-galactosamine galactosaminidase

hetero molecules

defined by author&software
Evidence: gel filtration
74.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: A type blood alpha-D-galactosamine galactosaminidase

hetero molecules

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

3

C: A type blood alpha-D-galactosamine galactosaminidase

hetero molecules

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

4

D: A type blood alpha-D-galactosamine galactosaminidase

hetero molecules

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

5

E: A type blood alpha-D-galactosamine galactosaminidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	103.676, 166.571, 133.210
Angle α, β, γ (deg.)	90.00, 90.21, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 5 molecules ABCDE

#1: Protein	A type blood alpha-D-galactosamine galactosaminidase / FpGalactosaminidase / FpGalNase / GH36 Mass: 73613.148 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavonifractor plautii (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P0DTR5, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

#1: Protein

A type blood alpha-D-galactosamine galactosaminidase / FpGalactosaminidase / FpGalNase / GH36

Mass: 73613.148 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Flavonifractor plautii (bacteria) / Production host:

Escherichia coli (E. coli)
References: UniProt: P0DTR5, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Non-polymers , 6 types, 2036 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#6: Chemical	ChemComp-A1AHC / 4-nitrophenyl 2-amino-2-deoxy-alpha-D-galactopyranoside Mass: 300.265 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₂H₁₆N₂O₇ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2011 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.64 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium chloride, 0.1 M Tris pH 8, 20% (w/v) PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18081 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 19, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.18081 Å / Relative weight: 1
Reflection	Resolution: 2.3→46.39 Å / Num. obs: 197617 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC_1/2: 0.996 / R_merge(I) obs: 0.083 / R_pim(I) all: 0.054 / R_rim(I) all: 0.099 / Χ²: 1.02 / Net I/σ(I): 12.8
Reflection shell	Resolution: 2.3→2.34 Å / % possible obs: 99.8 % / Redundancy: 3.3 % / R_merge(I) obs: 0.868 / Num. measured all: 32561 / Num. unique obs: 9830 / CC_1/2: 0.516 / R_pim(I) all: 0.563 / R_rim(I) all: 1.038 / Χ²: 0.8 / Net I/σ(I) obs: 1.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→46.39 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.908 / SU B: 11.683 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23374	9826	5 %	RANDOM
R_work	0.20683	-	-	-
obs	0.20818	187151	98.43 %	-

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 mean: 34.946 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.22 Å²	0 Å²	0.31 Å²
2-	-	0.17 Å²	-0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: 1 / Resolution: 2.3→46.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25335	0	125	2011	27471

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	26110
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	23160
X-RAY DIFFRACTION	r_angle_refined_deg	1.453	1.799	35590
X-RAY DIFFRACTION	r_angle_other_deg	0.52	1.748	53475
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.678	5	3265
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.984	5	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.008	10	3925
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	3770
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	31420
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6030
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	1.535	2.268	13075
X-RAY DIFFRACTION	r_mcbond_other	1.534	2.268	13075
X-RAY DIFFRACTION	r_mcangle_it	2.331	4.08	16335
X-RAY DIFFRACTION	r_mcangle_other	2.332	4.08	16336
X-RAY DIFFRACTION	r_scbond_it	2.223	2.475	13035
X-RAY DIFFRACTION	r_scbond_other	2.22	2.473	13032
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.458	4.469	19253
X-RAY DIFFRACTION	r_long_range_B_refined	5.399	28.07	112316
X-RAY DIFFRACTION	r_long_range_B_other	5.342	27.91	111001
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.382	762	-
R_work	0.357	13867	-
obs	-	-	99.61 %

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	2.3016	-0.389	0.048	2.1198	-0.0896	2.1614	0.0042	-0.0139	-0.1561	-0.0639	0.0257	0.3938	0.3048	-0.3752	-0.03	0.1543	-0.0503	-0.0499	0.2901	0.0241	0.192	20.214	-17.163	20.934
2	1.4933	0.0781	-0.1383	0.7039	-0.4368	1.491	0.0469	0.0174	-0.1747	-0.0456	0.0092	0.146	0.1769	-0.2453	-0.056	0.1016	-0.0086	-0.0327	0.0629	-0.006	0.072	33.808	-17.119	21.932
3	2.2146	1.376	0.7566	1.3802	1.0925	1.2948	0.1883	-0.2889	-0.0835	0.3416	-0.2547	0.0389	0.2027	-0.2779	0.0664	0.1702	-0.0163	0.0317	0.0941	0.0192	0.0458	35.084	-9.404	33.358
4	0.8893	0.5604	0.0108	2.2756	0.0176	0.9155	0.0219	-0.0838	-0.0451	-0.154	-0.0845	-0.3904	-0.0317	0.2618	0.0627	0.0688	0.0061	0.0037	0.1562	0.0268	0.0868	66.283	-5.343	41.922
5	0.6232	-0.1764	0.1206	0.4173	-0.1851	1.0105	0.0152	-0.1008	-0.0152	-0.0274	-0.0292	-0.0526	-0.0032	0.0854	0.014	0.0517	0.0034	-0.0016	0.0385	0.0084	0.0176	53.629	-4.703	36.017
6	1.6473	-0.8633	0.8894	3.9579	-0.4661	1.195	0.0117	0.0157	0.1756	-0.1281	-0.0069	-0.0369	-0.3241	-0.0778	-0.0048	0.1707	0.0247	0.0266	0.0555	0.0258	0.0624	41.073	16.991	18.637
7	1.2611	-0.1846	0.3236	2.1629	0.1635	2.1138	0.0508	-0.1806	0.0231	0.1388	0.0237	-0.1125	0.0037	0.2403	-0.0745	0.1562	0.0108	-0.0368	0.1852	-0.0199	0.0304	88.785	-30.258	33.909
8	0.846	-0.3128	0.0659	0.7869	0.0411	0.7182	0.0275	0.021	0.0966	-0.0372	0.012	-0.0499	-0.0799	0.033	-0.0395	0.0583	-0.0187	0.0006	0.0073	0.0027	0.0157	71.335	-21.301	6.833
9	1.9706	-0.3433	0.8713	2.1187	0.2008	1.8276	-0.0104	0.0368	-0.2652	-0.0303	0.0378	0.0478	0.3496	-0.026	-0.0274	0.1485	-0.0054	0.0001	0.0146	-0.0105	0.0528	71.735	-50.293	-0.489
10	1.9081	0.0599	0.4234	2.2497	0.0508	2.4119	0.0203	-0.2575	-0.4445	0.3006	0.0816	0.0293	0.5561	-0.0689	-0.1019	0.4268	-0.0934	0.0275	0.2556	0.0654	0.2935	105.091	-49.79	91.103
11	0.8953	-0.2403	-0.0922	1.4357	0.1479	0.9738	-0.0429	-0.2113	-0.2668	0.2668	0.0346	0.0294	0.2477	-0.0356	0.0082	0.185	-0.0476	-0.0067	0.169	0.0483	0.086	109.048	-36.069	87.654
12	1.4047	-0.5403	0.6948	1.1248	-0.4038	2.2615	0.0244	0.2125	0.2385	-0.0538	-0.0524	-0.1211	-0.2888	0.2706	0.0281	0.1483	-0.0665	0.0332	0.1269	0.0082	0.0668	111.766	0.924	81.843
13	0.5669	-0.0741	-0.0874	0.8188	0.5722	1.1998	0.0441	0.0612	-0.0051	0.0146	-0.0191	0.0322	-0.0266	-0.0288	-0.0251	0.0771	-0.031	-0.0007	0.109	0.0171	0.0072	104.552	-14.589	79.493
14	3.0033	-0.4852	0.2893	1.9736	0.1645	1.9364	0.0729	0.4068	-0.1695	-0.1266	-0.0876	0.3187	0.1666	-0.2863	0.0148	0.1583	-0.0265	-0.051	0.3126	-0.038	0.1005	89.838	-28.394	57.216
15	2.8459	-0.0627	0.7179	1.4485	0.4711	1.2918	-0.0709	-0.2653	0.4689	0.3397	-0.0059	-0.0014	-0.3921	0.0054	0.0769	0.3575	-0.0112	-0.008	0.3019	-0.091	0.211	41.632	9.265	82.123
16	1.265	0.3131	-0.0794	0.6471	-0.0552	0.6677	0.0085	0.0053	-0.0137	0.0123	-0.0498	0.017	0.026	-0.0035	0.0412	0.0965	-0.003	-0.0033	0.1152	0.015	0.0065	37.264	-19.886	64.954
17	1.8037	-0.0819	0.5365	3.197	-0.4081	2.2452	-0.0126	-0.3657	-0.1744	0.2777	-0.0278	-0.3508	0.2654	0.4558	0.0404	0.1707	0.0425	-0.0551	0.3387	0.0641	0.1301	63.204	-26.902	79.307
18	1.5744	0.5516	0.1898	2.4729	-0.1297	1.0418	-0.1016	0.0228	0.2453	-0.1151	0.2021	0.5629	-0.1606	-0.4534	-0.1006	0.2071	0.0315	-0.0022	0.379	0.1432	0.3791	73.035	10.717	-23.741
19	0.939	-0.2146	0.0427	1.095	-0.5477	1.417	-0.0009	0.0489	0.1153	-0.0385	0.1103	0.1892	-0.0374	-0.2704	-0.1093	0.0793	-0.0246	-0.0117	0.0949	0.0293	0.0817	89.36	2.675	-22.29
20	2.936	2.1148	1.1796	2.6755	0.8854	1.5662	-0.0338	0.092	-0.3841	-0.2187	0.0305	-0.4056	0.1752	0.3138	0.0032	0.1877	0.0386	-0.0103	0.1211	0.0211	0.1338	113.465	-23.62	-7.868
21	1.8524	0.4957	0.8168	1.6359	-0.076	2.6829	-0.0605	0.1603	-0.1533	-0.1953	0.0948	0.0538	0.281	-0.1249	-0.0344	0.1415	-0.054	0.0006	0.0522	-0.0022	0.0289	91.921	-23.481	-15.482
22	1.3622	0.4368	-0.4074	0.8138	-0.3775	0.9783	-0.0295	0.0505	-0.0574	-0.009	0.0369	0.0079	0.0742	0.0541	-0.0073	0.0766	-0.0229	-0.0171	0.0446	-0.006	0.0123	104.711	-4.994	-13.367
23	1.4091	0.0314	0.457	2.5952	0.431	1.7635	0.0422	-0.0554	0.1294	0.0769	0.0203	-0.0659	-0.1981	0.0926	-0.0624	0.0856	-0.0687	0.0021	0.0743	-0.015	0.0751	112.684	10.713	-10.992
24	1.9423	-1.5051	-0.3258	7.0934	2.6614	2.0784	0.035	0.1507	0.1999	-0.0679	-0.1188	-0.2322	-0.2551	0.0981	0.0838	0.1384	-0.065	-0.0193	0.1334	-0.0069	0.143	118.741	17.945	-9.197

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	44 - 109
2	X-RAY DIFFRACTION	2	A	110 - 257
3	X-RAY DIFFRACTION	3	A	258 - 312
4	X-RAY DIFFRACTION	4	A	313 - 421
5	X-RAY DIFFRACTION	5	A	422 - 599
6	X-RAY DIFFRACTION	6	A	600 - 697
7	X-RAY DIFFRACTION	7	B	44 - 166
8	X-RAY DIFFRACTION	8	B	167 - 582
9	X-RAY DIFFRACTION	9	B	583 - 697
10	X-RAY DIFFRACTION	10	C	44 - 109
11	X-RAY DIFFRACTION	11	C	110 - 312
12	X-RAY DIFFRACTION	12	C	313 - 421
13	X-RAY DIFFRACTION	13	C	422 - 634
14	X-RAY DIFFRACTION	14	C	635 - 697
15	X-RAY DIFFRACTION	15	D	44 - 166
16	X-RAY DIFFRACTION	16	D	167 - 599
17	X-RAY DIFFRACTION	17	D	600 - 697
18	X-RAY DIFFRACTION	18	E	44 - 166
19	X-RAY DIFFRACTION	19	E	167 - 312
20	X-RAY DIFFRACTION	20	E	313 - 380
21	X-RAY DIFFRACTION	21	E	381 - 502
22	X-RAY DIFFRACTION	22	E	503 - 582
23	X-RAY DIFFRACTION	23	E	583 - 663
24	X-RAY DIFFRACTION	24	E	664 - 697

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Protein , 1 types, 5 molecules ABCDE

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Non-polymers , 6 types, 2036 molecules

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-Protein , 1 types, 5 molecules ABCDE

-Non-polymers , 6 types, 2036 molecules

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-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 5 molecules ABCDE

-
Non-polymers , 6 types, 2036 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi