PDB-9ay8: Structure of the A type blood alpha-D-galactosamine galactosamini...

ID or keywords:

Entry

Database: PDB / ID: 9ay8

Title

Structure of the A type blood alpha-D-galactosamine galactosaminidase 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 7, 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	9ay8.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb9ay8.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	9ay8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ay8_validation.pdf.gz	472.6 KB	Display	wwPDB validaton report
Full document	9ay8_full_validation.pdf.gz	487.1 KB	Display
Data in XML	9ay8_validation.xml.gz	165 KB	Display
Data in CIF	9ay8_validation.cif.gz	235.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ay/9ay8 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/9ay8	HTTPS FTP

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Related structure data

Related structure data	9awtC 9ayuC 9aww PDB Unreleased entry 9ax4 PDB Unreleased entry 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

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
74.1 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
73.8 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
73.8 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)	102.685, 164.568, 131.645
Angle α, β, γ (deg.)	90.00, 90.30, 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, 3359 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#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
#5: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#6: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3337 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 3.02 Å³/Da / Density % sol: 59.3 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BICINE pH 9, 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: 1.1806 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 27, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1806 Å / Relative weight: 1
Reflection	Resolution: 2→39.44 Å / Num. obs: 290235 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.063 / R_pim(I) all: 0.04 / R_rim(I) all: 0.075 / Χ²: 1.1 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2→2.03 Å / % possible obs: 98.7 % / Redundancy: 3.4 % / R_merge(I) obs: 1.244 / Num. measured all: 48915 / Num. unique obs: 14258 / CC_1/2: 0.403 / R_pim(I) all: 0.781 / R_rim(I) all: 1.472 / Χ²: 0.92 / Net I/σ(I) obs: 1

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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→39.44 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.957 / SU B: 6.521 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1933	14518	5 %	RANDOM
R_work	0.16772	-	-	-
obs	0.169	275678	98.71 %	-

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: 33.934 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0 Å²	0.07 Å²
2-	-	0.32 Å²	0 Å²
3-	-	-	-0.12 Å²

Refinement step

Cycle: 1 / Resolution: 2→39.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25335	0	50	3337	28722

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	26045
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	23151
X-RAY DIFFRACTION	r_angle_refined_deg	1.465	1.794	35496
X-RAY DIFFRACTION	r_angle_other_deg	0.516	1.744	53450
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.771	5	3268
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.314	5	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.853	10	3930
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	3753
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	31378
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6012
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	1.527	1.994	13081
X-RAY DIFFRACTION	r_mcbond_other	1.527	1.994	13081
X-RAY DIFFRACTION	r_mcangle_it	2.141	3.573	16343
X-RAY DIFFRACTION	r_mcangle_other	2.141	3.573	16344
X-RAY DIFFRACTION	r_scbond_it	2.472	2.197	12964
X-RAY DIFFRACTION	r_scbond_other	2.441	2.195	12962
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.664	3.946	19153
X-RAY DIFFRACTION	r_long_range_B_refined	5.647	26.09	121830
X-RAY DIFFRACTION	r_long_range_B_other	5.645	26.05	121697
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	0.426	1041	-
R_work	0.42	20267	-
obs	-	-	98.4 %

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	1.9552	0.0735	-0.0522	2.4363	-0.3238	2.4005	0.0839	0.0573	-0.2097	-0.0511	-0.0277	0.4556	0.228	-0.4601	-0.0563	0.085	-0.0568	-0.0454	0.3374	0.0023	0.2447	20.11	-17.254	20.605
2	1.3181	-0.0406	-0.2277	0.8921	-0.2754	1.603	0.026	0.0293	-0.1825	-0.0412	-0.0012	0.2293	0.2068	-0.2828	-0.0249	0.0789	-0.0239	-0.0284	0.1194	0.0044	0.091	33.516	-17.152	21.593
3	1.907	0.921	0.3342	1.3536	0.461	0.9959	0.129	-0.2258	-0.1572	0.2357	-0.1775	0.0585	0.1655	-0.2457	0.0485	0.1119	-0.0091	0.0061	0.1396	0.0233	0.056	34.728	-9.512	32.862
4	0.8929	0.4572	-0.0555	2.4337	-0.3069	0.8886	0.0192	-0.1157	-0.0279	-0.0623	-0.0796	-0.389	-0.0386	0.3078	0.0604	0.0721	0.0051	-0.0189	0.2076	0.0256	0.0861	65.467	-5.361	41.386
5	0.4491	-0.0907	0.0504	0.7548	-0.3181	1.3132	0.0014	-0.1032	-0.0107	-0.0016	-0.0207	-0.1181	0.0009	0.0832	0.0194	0.0401	0.0059	-0.005	0.0895	0.0146	0.036	52.964	-4.825	35.481
6	1.4246	-0.6452	0.6052	3.5459	-0.3081	1.1474	0.0095	0.0367	0.1727	-0.098	-0.0058	-0.0057	-0.3409	-0.0993	-0.0036	0.1504	0.0405	0.0172	0.0966	0.0305	0.0702	40.498	16.538	18.318
7	1.6246	-0.1539	0.1664	2.2208	0.3559	1.8676	0.0621	-0.2929	0.0343	0.1987	-0.0274	-0.1537	0.0193	0.244	-0.0347	0.1783	0.0002	-0.0792	0.2605	-0.0044	0.04	87.857	-29.763	33.403
8	0.9132	-0.3013	-0.0304	0.9134	0.0739	0.7479	0.0556	0.0234	0.1254	-0.0478	-0.0045	-0.0736	-0.0592	0.0281	-0.0511	0.0464	-0.0163	0.0031	0.0484	0.0079	0.0235	70.627	-21.147	6.657
9	1.7205	-0.0814	0.7959	1.9518	0.2403	2.143	-0.049	0.047	-0.2757	-0.0573	0.0461	0.0274	0.4172	-0.0143	0.0029	0.1888	-0.0061	0.012	0.0535	-0.0086	0.066	71.23	-49.764	-0.53
10	1.5942	-0.2617	0.7631	1.7375	0.4047	2.5733	-0.0426	-0.2358	-0.6438	0.2793	0.1311	0.1598	0.585	-0.161	-0.0885	0.4985	-0.15	0.0606	0.307	0.1291	0.3861	103.648	-49.008	89.83
11	1.0413	-0.324	-0.0716	1.6523	0.1482	1.2401	-0.0764	-0.2085	-0.346	0.2329	0.0824	0.093	0.3262	-0.0809	-0.006	0.2346	-0.1052	-0.0001	0.2409	0.0839	0.118	107.653	-35.538	86.424
12	1.3862	-0.4593	0.6683	1.1434	-0.3154	2.1685	0.0481	0.2417	0.3048	-0.1173	-0.0375	-0.1776	-0.3359	0.2349	-0.0105	0.175	-0.0982	0.0321	0.2396	0.0378	0.0947	110.477	0.977	80.797
13	0.5869	-0.1816	-0.1407	0.7801	0.6828	1.5556	0.0389	0.0689	0.0138	-0.0399	-0.0227	0.0411	-0.007	-0.093	-0.0161	0.0993	-0.0856	-0.0216	0.2214	0.0413	0.0125	103.377	-14.36	78.387
14	3.7136	-0.3039	0.7087	1.5412	0.3289	1.7755	0.1056	0.3555	-0.2704	-0.1645	-0.1942	0.379	0.1255	-0.4276	0.0887	0.2609	-0.0823	-0.1019	0.4499	-0.0365	0.1539	88.907	-27.863	56.301
15	2.8775	-0.2244	0.3912	1.0756	0.3955	1.6538	-0.0563	-0.3301	0.4892	0.2147	0.0409	-0.0173	-0.4353	0.0095	0.0153	0.3434	-0.0067	-0.0566	0.3399	-0.1197	0.2157	40.911	8.885	81.05
16	1.4087	0.2716	-0.1552	0.6376	-0.0687	0.8522	-0.0336	-0.0166	-0.0503	0.0332	-0.0252	-0.0191	0.1087	0.0045	0.0588	0.1401	-0.0089	-0.0181	0.1754	0.0293	0.0146	36.626	-19.802	64.043
17	1.8497	-0.0299	1.1594	3.4076	-0.8885	2.5744	-0.012	-0.3263	-0.2304	0.2557	-0.0796	-0.4524	0.3744	0.5828	0.0917	0.2668	0.1357	-0.0632	0.5119	0.1047	0.1612	62.182	-26.732	78.222
18	1.9453	0.7696	0.0395	2.2657	-0.2295	0.9109	-0.0675	0.042	0.3347	-0.1075	0.149	0.477	-0.2603	-0.5024	-0.0814	0.222	0.0652	-0.0086	0.4386	0.1571	0.3955	72.282	10.181	-23.554
19	1.0522	0.042	-0.037	1.2953	-0.5089	1.4559	0.0095	0.1149	0.2075	-0.0243	0.1568	0.2766	-0.0831	-0.3072	-0.1663	0.0735	-0.0266	-0.0137	0.1831	0.0728	0.102	88.474	2.416	-22.107
20	3.0566	1.3723	0.8709	2.4991	0.4844	1.7021	-0.0291	0.0249	-0.5589	-0.0568	0.031	-0.4422	0.2737	0.3489	-0.0019	0.1502	0.0333	-0.009	0.178	0.0199	0.1804	112.419	-23.414	-7.798
21	1.9984	0.8715	0.5248	1.7031	-0.323	2.3588	-0.0788	0.214	-0.1841	-0.2135	0.1695	0.0341	0.3243	-0.092	-0.0908	0.1434	-0.0692	-0.0226	0.1242	-0.005	0.0298	91.109	-23.341	-15.334
22	1.5335	0.6221	-0.4125	1.2934	-0.6557	1.3953	0.0301	0.0825	-0.0034	0.0638	0.0341	0.0072	-0.0206	0.0515	-0.0642	0.0677	-0.0485	-0.0134	0.0938	-0.0085	0.011	103.663	-5.054	-13.33
23	1.5669	0.0832	0.2873	2.3958	0.2594	1.6388	0.0687	-0.0281	0.2357	0.16	-0.0185	-0.0769	-0.2635	0.1029	-0.0502	0.1142	-0.091	0.002	0.1423	-0.0164	0.0842	111.456	10.464	-10.97
24	2.4515	-1.0104	-0.0621	6.0351	3.102	3.0145	0.1076	0.1857	0.1553	-0.1677	-0.0796	-0.2138	-0.361	0.1753	-0.028	0.1863	-0.117	0.0019	0.1713	-0.0068	0.1487	117.427	17.649	-9.248

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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Protein , 1 types, 5 molecules ABCDE

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Non-polymers , 6 types, 3359 molecules

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Structure viewers

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Viewer log

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Components

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Protein , 1 types, 5 molecules ABCDE

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Non-polymers , 6 types, 3359 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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Yorodumi