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

ID or keywords:

Entry

Database: PDB / ID: 9ayu

Title

Structure of the A type blood alpha-D-galactosamine galactosaminidase D463A mutant from Flavonifractor plautii

Components

A type blood alpha-D-galactosamine galactosaminidase

Keywords

SUGAR BINDING PROTEIN / galactosaminidase

Function / homology

Melibiase / : / alpha-galactosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / : / A type blood alpha-D-galactosamine galactosaminidase

Function and homology information

Biological species

Flavonifractor plautii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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 8, 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	9ayu.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb9ayu.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	9ayu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ayu_validation.pdf.gz	479.9 KB	Display	wwPDB validaton report
Full document	9ayu_full_validation.pdf.gz	500.8 KB	Display
Data in XML	9ayu_validation.xml.gz	163.6 KB	Display
Data in CIF	9ayu_validation.cif.gz	229.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ay/9ayu ftp://data.pdbj.org/pub/pdb/validation_reports/ay/9ayu	HTTPS FTP

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Related structure data

Related structure data	9awtC 9ay8C 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

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

370 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
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 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
73.9 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
73.9 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
73.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.326, 164.290, 131.763
Angle α, β, γ (deg.)	90.00, 90.20, 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: 73569.141 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: 73569.141 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 , 5 types, 3107 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3074 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 3.01 Å³/Da / Density % sol: 59.15 %
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: 08ID-1 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2→48.9 Å / Num. obs: 292440 / % possible obs: 100 % / Redundancy: 4.4 % / CC_1/2: 0.992 / R_merge(I) obs: 0.17 / R_pim(I) all: 0.09 / R_rim(I) all: 0.193 / Χ²: 1 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2→2.03 Å / % possible obs: 100 % / Redundancy: 4.5 % / R_merge(I) obs: 1.256 / Num. measured all: 65499 / Num. unique obs: 14443 / CC_1/2: 0.48 / R_pim(I) all: 0.661 / R_rim(I) all: 1.422 / Χ²: 1 / 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→48.9 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.951 / SU B: 6.81 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18617	14623	5 %	RANDOM
R_work	0.16284	-	-	-
obs	0.16401	277769	99.94 %	-

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: 24.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	-0 Å²	0.39 Å²
2-	-	0.17 Å²	0 Å²
3-	-	-	-0.18 Å²

Refinement step

Cycle: 1 / Resolution: 2→48.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25320	0	87	3074	28481

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	26173
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	23295
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.794	35639
X-RAY DIFFRACTION	r_angle_other_deg	0.546	1.743	53752
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.942	5	3281
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.953	5	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.657	10	3930
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	3755
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	31557
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6069
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	0.795	0.988	13133
X-RAY DIFFRACTION	r_mcbond_other	0.794	0.988	13133
X-RAY DIFFRACTION	r_mcangle_it	1.3	1.769	16411
X-RAY DIFFRACTION	r_mcangle_other	1.3	1.769	16412
X-RAY DIFFRACTION	r_scbond_it	1.527	1.118	13040
X-RAY DIFFRACTION	r_scbond_other	1.527	1.118	13041
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.395	1.984	19229
X-RAY DIFFRACTION	r_long_range_B_refined	4.635	13.14	119815
X-RAY DIFFRACTION	r_long_range_B_other	4.336	12.23	116755
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.281	1047	-
R_work	0.278	20481	-
obs	-	-	99.98 %

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	1.9929	-0.296	0.3081	1.8914	-0.4269	3.1379	0.0724	0.0379	-0.2562	-0.0679	0.0153	0.3966	0.3593	-0.5487	-0.0877	0.1274	-0.0813	0.0019	0.3343	0.0276	0.2607	19.717	-16.92	20.967
2	1.3225	0.1402	-0.0491	0.9376	-0.2695	1.8044	0.0081	0.009	-0.19	-0.0507	0.0309	0.2096	0.2641	-0.3259	-0.039	0.1207	-0.0186	0.0279	0.0926	0.0202	0.1158	33.174	-16.91	21.879
3	1.9164	1.0925	0.4897	1.2918	0.7377	1.2863	0.1273	-0.2859	-0.1026	0.2403	-0.1803	0.0669	0.1816	-0.2896	0.053	0.1271	0.0006	0.0475	0.1146	0.0424	0.0789	34.501	-9.21	33.14
4	0.9741	0.473	0.1088	2.1446	-0.1637	1.0059	0.0154	-0.1204	-0.0315	-0.1223	-0.0652	-0.3975	-0.0389	0.3446	0.0498	0.1007	0.008	0.0497	0.1933	0.0287	0.0879	65.445	-5.26	41.465
5	0.6942	-0.2067	0.1021	0.6099	-0.2867	1.3954	0.0091	-0.1313	-0.0255	0.0008	-0.0127	-0.046	-0.0099	0.1046	0.0035	0.0673	0.0098	0.0468	0.0584	0.0166	0.0398	52.852	-4.635	35.672
6	1.5692	-0.7461	0.8324	3.2764	-0.1687	1.3574	0.0034	0.0319	0.1821	-0.0773	-0.0126	0.0282	-0.3513	-0.0907	0.0092	0.1769	0.0332	0.0573	0.0624	0.022	0.09	40.501	16.772	18.457
7	1.3008	-0.429	0.2195	1.887	0.134	2.2236	0.0313	-0.2595	-0.0044	0.1368	0.0225	-0.1617	-0.0024	0.3041	-0.0537	0.1767	0.0116	-0.0156	0.2229	-0.007	0.0234	87.6	-29.738	33.498
8	0.9102	-0.2995	0.0311	0.8666	0.0073	0.9065	0.0418	-0.0037	0.0929	-0.0348	0.0106	-0.0345	-0.0647	0.0037	-0.0524	0.077	-0.0061	0.0327	0.0019	-0.0021	0.0215	70.245	-21.05	6.755
9	1.4868	0.02	0.6015	2.1112	0.159	1.9832	0.0102	0.0283	-0.2311	-0.0678	-0.013	0.0368	0.4242	-0.0158	0.0028	0.1978	-0.0108	0.0224	0.0173	0.002	0.046	70.783	-49.657	-0.474
10	1.381	0.0756	0.5654	2.5712	0.5852	3.158	0.0193	-0.235	-0.4649	0.319	0.0228	0.0201	0.6875	-0.1313	-0.0421	0.426	-0.1205	0.0761	0.221	0.0904	0.2493	103.515	-49.1	90.096
11	0.9727	-0.1628	-0.2113	1.6169	0.1449	1.353	-0.0388	-0.1764	-0.2546	0.2467	0.0103	0.0031	0.3077	-0.044	0.0285	0.1978	-0.0675	0.0259	0.1575	0.0356	0.0755	107.469	-35.535	86.704
12	1.2309	-0.4594	0.3871	1.093	-0.0098	1.9174	0.0476	0.1965	0.3185	-0.0985	-0.0369	-0.1936	-0.4065	0.1836	-0.0107	0.2107	-0.0697	0.0729	0.1391	0.0381	0.1045	110.226	1.072	80.994
13	0.6245	-0.038	-0.2012	0.8692	0.6293	1.4517	0.0556	0.093	0.0252	-0.013	-0.0341	0.0219	-0.0714	-0.0809	-0.0214	0.0983	-0.0273	0.0344	0.142	0.0174	0.0193	103.074	-14.279	78.645
14	2.5674	-0.4912	0.5441	1.73	0.5109	1.9084	0.1171	0.4394	-0.2173	-0.2146	-0.193	0.3106	0.0929	-0.4058	0.0759	0.1913	-0.0286	-0.019	0.4162	-0.0487	0.1024	88.588	-27.901	56.558
15	3.2437	0.1403	0.6094	1.8128	0.5156	1.4713	-0.0584	-0.3523	0.5243	0.3274	-0.0167	0.0236	-0.5098	-0.0056	0.0751	0.4486	-0.0094	0.043	0.3189	-0.1222	0.2077	41.098	9.284	81.2
16	1.3825	0.3552	-0.1543	0.7178	-0.1357	0.7624	-0.0156	0.0046	-0.038	0.0126	-0.0279	-0.0026	0.0297	0.0091	0.0434	0.1171	0.0027	0.0392	0.1544	0.0224	0.0182	36.764	-19.576	64.312
17	2.1941	-0.122	0.5529	2.4843	-0.198	1.6965	-0.0144	-0.4296	-0.2324	0.2856	-0.0311	-0.3569	0.2458	0.4704	0.0455	0.2135	0.0558	-0.0211	0.429	0.0903	0.1444	62.413	-26.5	78.472
18	1.6442	0.8284	-0.4477	3.7103	-1.1591	1.4486	-0.0563	0.2091	0.4088	-0.1158	0.529	1.0015	-0.2665	-0.7063	-0.4727	0.2142	0.0921	0.0574	0.4177	0.2985	0.5758	72.013	11.03	-23.159
19	1.0899	0.0764	-0.1731	1.5972	-0.8034	1.74	0.0203	0.1091	0.187	-0.0459	0.2144	0.3039	-0.0983	-0.3218	-0.2348	0.0949	-0.0073	0.0351	0.0832	0.0658	0.1116	88.105	2.865	-21.949
20	2.7987	1.6577	0.658	2.6391	0.0902	1.3352	-0.0642	-0.0011	-0.4698	-0.1391	-0.0126	-0.5483	0.2143	0.3971	0.0768	0.1658	0.0472	0.0439	0.1469	0.0474	0.158	111.881	-23.419	-7.894
21	1.8461	0.5056	0.2448	1.5933	-0.4195	2.2845	-0.0726	0.1259	-0.1162	-0.2192	0.1315	0.0739	0.3419	-0.1732	-0.0588	0.169	-0.0545	0.0268	0.0424	0.0006	0.0325	90.445	-23.011	-15.309
22	1.1498	0.6584	-0.2403	1.3917	-0.4119	1.0178	0.0401	0.002	0.0281	0.0458	0.0308	-0.0106	-0.0246	0.0842	-0.0709	0.0844	-0.0194	0.0237	0.0325	-0.0121	0.0135	103.279	-4.88	-13.231
23	1.4278	0.196	0.5387	2.1491	0.3102	1.2323	0.0714	-0.0679	0.1993	0.0974	-0.0385	-0.0982	-0.2528	0.1717	-0.0329	0.1692	-0.07	0.0572	0.0897	-0.0288	0.0971	111.26	10.571	-10.876
24	2.0857	-0.7297	0.141	7.02	3.5196	2.3227	0.0572	0.123	0.119	-0.1737	0.0459	-0.2208	-0.3528	0.2443	-0.1031	0.2176	-0.0839	0.0259	0.1328	-0.0102	0.1613	117.27	17.655	-9.162

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	44 - 83
2	X-RAY DIFFRACTION	2	A	84 - 231
3	X-RAY DIFFRACTION	3	A	232 - 286
4	X-RAY DIFFRACTION	4	A	287 - 395
5	X-RAY DIFFRACTION	5	A	396 - 573
6	X-RAY DIFFRACTION	6	A	574 - 671
7	X-RAY DIFFRACTION	7	B	44 - 140
8	X-RAY DIFFRACTION	8	B	141 - 556
9	X-RAY DIFFRACTION	9	B	557 - 671
10	X-RAY DIFFRACTION	10	C	44 - 83
11	X-RAY DIFFRACTION	11	C	84 - 286
12	X-RAY DIFFRACTION	12	C	287 - 395
13	X-RAY DIFFRACTION	13	C	396 - 608
14	X-RAY DIFFRACTION	14	C	609 - 671
15	X-RAY DIFFRACTION	15	D	44 - 140
16	X-RAY DIFFRACTION	16	D	141 - 573
17	X-RAY DIFFRACTION	17	D	574 - 671
18	X-RAY DIFFRACTION	18	E	44 - 140
19	X-RAY DIFFRACTION	19	E	141 - 286
20	X-RAY DIFFRACTION	20	E	287 - 354
21	X-RAY DIFFRACTION	21	E	355 - 476
22	X-RAY DIFFRACTION	22	E	477 - 556
23	X-RAY DIFFRACTION	23	E	557 - 637
24	X-RAY DIFFRACTION	24	E	638 - 671

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 5 molecules ABCDE

-
Non-polymers , 5 types, 3107 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi