PDB-8zyi: crystal structure of GH57 family amylopullulanase mutant D352N fr...

ID or keywords:

Entry

Database: PDB / ID: 8zyi

Title

crystal structure of GH57 family amylopullulanase mutant D352N from Aquifex aeolicus in complex wih 6-alpha-D-maltotriosyl-maltotriose

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 / Amylopullulanase / Complex

Function / homology

: / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / catalytic activity / carbohydrate metabolic process / Glycoside hydrolase family 57 N-terminal domain-containing protein

Function and homology information

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.657 Å

Authors

Zhu, Z.M. / Wang, W.W. / Yu, F.

Funding support

China, 2items

Citation

Journal: Commun Biol / Year: 2025
Title: The crystal structure of GH57 family amylopullulanase reveals its dual binding pockets sharing the same catalytic dyad.
Authors: Zhu, Z. / Wang, W. / Li, M. / Xu, Q. / Zhou, H. / Huang, L. / Wang, Q. / Yu, F.

History

Deposition	Jun 17, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jun 4, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8zyi.cif.gz	422.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8zyi.ent.gz	348.2 KB	Display	PDB format
PDBx/mmJSON format	8zyi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8zyi_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8zyi_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8zyi_validation.xml.gz	49.6 KB	Display
Data in CIF	8zyi_validation.cif.gz	68 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zy/8zyi ftp://data.pdbj.org/pub/pdb/validation_reports/zy/8zyi	HTTPS FTP

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Related structure data

Related structure data	9ihtC 9ihuC 9ihvC 9ihwC 9ihxC 9ii0C 9ii1C 9k7cC 9k7dC 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	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (2)

Deposited unit

A: Glycoside hydrolase family 57 N-terminal domain-containing protein

B: Glycoside hydrolase family 57 N-terminal domain-containing protein

hetero molecules

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

1

A: Glycoside hydrolase family 57 N-terminal domain-containing protein

hetero molecules

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

2

B: Glycoside hydrolase family 57 N-terminal domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.786, 41.518, 194.510
Angle α, β, γ (deg.)	90.00, 96.08, 90.00
Int Tables number	3
Space group name H-M	P121

#1: Protein

Glycoside hydrolase family 57 N-terminal domain-containing protein

Mass: 57252.250 Da / Num. of mol.: 2 / Mutation: D352N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aquifex aeolicus (strain VF5) (bacteria)
Gene: aq_720 / Production host:

Escherichia coli (E. coli) / References: UniProt: O66934

#2: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D- ...

Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-6DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b6-c1_c4-d1_d4-e1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H₂O

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: 2.14 Å³/Da / Density % sol: 42.42 %
Crystal grow	Temperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium citrate, 25% PEG 3350, pH4.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 13, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection	Resolution: 1.657→96.71 Å / Num. obs: 117555 / % possible obs: 100 % / Redundancy: 5.8 % / CC_1/2: 0.994 / R_merge(I) obs: 0.142 / R_pim(I) all: 0.064 / R_rim(I) all: 0.156 / Χ²: 0.84 / Net I/σ(I): 7.7
Reflection shell	Resolution: 1.66→1.75 Å / % possible obs: 100 % / Redundancy: 5.8 % / R_merge(I) obs: 1.829 / Num. measured all: 98447 / Num. unique obs: 16973 / CC_1/2: 0.487 / R_pim(I) all: 0.827 / R_rim(I) all: 2.012 / Χ²: 0.72 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.657→40.118 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2014	5885	5.06 %
R_work	0.1696	-	-
obs	0.1712	116208	98.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.657→40.118 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8200	0	0	669	8869

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8434
X-RAY DIFFRACTION	f_angle_d	0.937	11424
X-RAY DIFFRACTION	f_dihedral_angle_d	6.136	5026
X-RAY DIFFRACTION	f_chiral_restr	0.053	1218
X-RAY DIFFRACTION	f_plane_restr	0.006	1424

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6572-1.676	0.2898	164	0.2741	3103	X-RAY DIFFRACTION	85
1.676-1.6958	0.3117	173	0.2668	3376	X-RAY DIFFRACTION	91
1.6958-1.7164	0.2864	193	0.2662	3575	X-RAY DIFFRACTION	96
1.7164-1.7382	0.2922	217	0.2542	3531	X-RAY DIFFRACTION	96
1.7382-1.761	0.2786	183	0.2453	3604	X-RAY DIFFRACTION	99
1.761-1.7852	0.2716	199	0.2358	3663	X-RAY DIFFRACTION	99
1.7852-1.8107	0.2597	208	0.2417	3702	X-RAY DIFFRACTION	99
1.8107-1.8377	0.2429	205	0.2294	3586	X-RAY DIFFRACTION	100
1.8377-1.8664	0.2752	223	0.2189	3737	X-RAY DIFFRACTION	100
1.8664-1.897	0.2318	187	0.2005	3683	X-RAY DIFFRACTION	100
1.897-1.9297	0.2366	184	0.1952	3673	X-RAY DIFFRACTION	100
1.9297-1.9648	0.2135	203	0.1858	3724	X-RAY DIFFRACTION	100
1.9648-2.0026	0.2256	183	0.1827	3717	X-RAY DIFFRACTION	100
2.0026-2.0435	0.2197	226	0.1746	3645	X-RAY DIFFRACTION	100
2.0435-2.0879	0.2047	196	0.1762	3715	X-RAY DIFFRACTION	100
2.0879-2.1365	0.2135	189	0.1688	3727	X-RAY DIFFRACTION	100
2.1365-2.1899	0.1815	196	0.169	3748	X-RAY DIFFRACTION	100
2.1899-2.2491	0.2026	191	0.1672	3656	X-RAY DIFFRACTION	100
2.2491-2.3153	0.2106	218	0.1614	3713	X-RAY DIFFRACTION	100
2.3153-2.39	0.1908	213	0.161	3683	X-RAY DIFFRACTION	100
2.39-2.4754	0.2013	197	0.1674	3749	X-RAY DIFFRACTION	100
2.4754-2.5745	0.2009	163	0.1623	3779	X-RAY DIFFRACTION	100
2.5745-2.6916	0.2164	162	0.1602	3700	X-RAY DIFFRACTION	100
2.6916-2.8335	0.1906	170	0.1686	3781	X-RAY DIFFRACTION	100
2.8335-3.011	0.2018	187	0.1653	3737	X-RAY DIFFRACTION	100
3.011-3.2434	0.1777	228	0.1606	3766	X-RAY DIFFRACTION	100
3.2434-3.5696	0.1739	201	0.1523	3724	X-RAY DIFFRACTION	100
3.5696-4.0857	0.1688	217	0.1296	3774	X-RAY DIFFRACTION	100
4.0857-5.1458	0.1523	215	0.1255	3815	X-RAY DIFFRACTION	100
5.1458-40.118	0.1824	194	0.1586	3937	X-RAY DIFFRACTION	100

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	0.9634	-0.0583	-0.3441	0.3639	0.1302	1.1561	-0.0435	-0.0411	-0.109	-0.0064	0.0354	0.0375	0.1283	-0.1263	0.0154	0.0854	-0.0215	0.0064	0.0485	-0.0013	0.1316	-12.7947	14.7696	74.1355
2	2.1495	0.1565	-0.9637	1.306	-0.1397	3.1399	0.0877	-0.0596	0.3629	0.0581	-0.0455	0.1364	-0.3965	-0.1764	0.0139	0.1183	0.0073	0.0208	0.0914	-0.0041	0.2061	-25.4447	28.2436	81.3639
3	0.9177	-0.0989	-0.2133	0.2616	-0.0465	0.8695	-0.0571	0.0725	-0.0887	-0.06	0.0204	-0.0503	0.0764	0.0955	0.0023	0.1222	-0.0255	0.0195	0.0459	-0.025	0.1602	1.9626	14.3298	66.6002
4	1.9381	0.0612	-0.5974	1.4549	0.0499	2.2987	0.0117	0.3189	0.0311	-0.2712	0.0353	0.0613	-0.1122	-0.0798	-0.0527	0.1542	-0.038	-0.007	0.0913	0.0026	0.1083	-7.8121	23.4643	52.7408
5	1.1995	0.0265	-0.0055	1.0746	0.0502	3.124	-0.0323	-0.0968	0.0545	0.0358	0.0068	-0.0793	-0.2056	0.2512	0.0464	0.0322	-0.0172	0.0079	0.1108	-0.0176	0.1512	12.3073	20.8696	75.9229
6	4.1569	0.0481	-0.559	1.759	0.8658	4.1151	-0.0856	-0.3451	0.0666	0.058	0.0059	0.0972	-0.1092	-0.0035	0.0241	0.0341	-0.0139	-0.0036	0.1107	-0.013	0.0979	1.9685	17.3297	86.347
7	1.0311	0.1042	-0.5232	0.5123	-0.2273	0.3531	-0.0188	0.1408	-0.1139	-0.0572	0.0735	-0.0493	0.5192	0.6153	-0.0483	0.1997	0.1328	-0.0342	0.2585	-0.0774	0.1471	-26.3526	34.2677	26.6338
8	0.7417	0.4769	-0.9863	1.0826	-0.1678	2.4578	-0.0243	0.4145	0.0428	0.0106	0.0056	0.1175	0.1043	0.2269	0.0104	0.2725	0.0502	-0.0506	0.5879	-0.0369	0.1901	-19.9507	39.905	5.5249
9	2.0772	-0.0419	-0.9641	0.6917	0.8637	2.806	0.0552	0.2792	0.3521	-0.0513	0.0532	-0.2594	-0.6555	0.9875	-0.0091	0.282	-0.0854	0.0006	0.6434	-0.0253	0.2445	-10.7533	47.3726	14.0188
10	1.2824	0.0139	-0.2175	0.6275	-0.1165	2.0745	-0.1496	0.3342	-0.307	0.2117	0.0936	-0.1589	0.5307	0.7893	0.0302	0.2629	0.3801	0.0256	0.5189	-0.1133	0.1957	-14.87	29.9785	22.2684
11	2.1461	0.116	0.0208	1.0383	-0.0457	1.9418	0.0073	0.1413	-0.2621	-0.0067	0.1091	0.1873	0.591	-0.4588	-0.0402	0.3044	0.0224	-0.0543	0.2269	-0.0776	0.1683	-45.3048	31.3144	26.9936
12	2.8704	-0.933	-1.1354	2.9728	0.0879	1.7862	-0.0468	0.0884	-0.3438	0.3236	0.0992	-0.1109	0.7751	-0.0898	-0.0324	0.3537	0.0083	-0.0596	0.1749	-0.0584	0.1679	-43.1271	30.0169	35.8946
13	2.0568	0.9464	-0.7111	0.9283	-0.6564	2.4812	-0.0128	-0.2001	0.2046	-0.0537	-0.0334	0.1425	-0.2229	-0.1173	-0.008	0.1679	0.0551	-0.0226	0.1181	-0.058	0.1708	-39.635	44.1345	41.7814
14	1.7089	0.209	-0.8119	1.1076	-0.2599	3.545	0.0838	-0.2061	0.2008	0.1153	-0.0888	0.0684	-0.5386	0.2522	0.0003	0.2315	0.0203	-0.0214	0.1746	-0.0671	0.1431	-28.0946	47.7539	42.4476
15	2.2681	0.2298	-0.2158	0.7523	0.0782	3.5662	0.013	-0.1603	-0.0194	0.0994	0.0305	-0.0555	0.0335	0.5681	-0.0145	0.1704	0.0739	-0.0352	0.2735	-0.0736	0.1368	-24.0921	39.8631	45.0823
16	1.3881	0.1369	0.8089	1.1191	-0.1394	3.2693	-0.0178	0.3199	0.1168	-0.1444	0.1043	0.1692	-0.0978	-0.4917	-0.0127	0.1204	0.0315	-0.0322	0.3027	-0.0139	0.198	-49.5551	40.7104	24.2064
17	4.0146	-0.1728	0.2549	2.4302	-0.5135	4.325	-0.1107	0.5062	0.1195	-0.0854	0.0957	0.0093	0.2144	-0.241	0.0017	0.1963	0.0233	-0.0564	0.3408	-0.0364	0.1202	-41.0799	36.6622	12.3828

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 88 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 158 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 159 through 322 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 323 through 396 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 397 through 435 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 436 through 477 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 68 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 69 through 102 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 103 through 158 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 159 through 185 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 186 through 245 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 246 through 278 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 279 through 322 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 323 through 360 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 361 through 396 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 397 through 435 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 436 through 477 )

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