PDB-9ihx: Co-crystal structure of GH57 family amylopullulanase wild type fr...

ID or keywords:

Entry

Database: PDB / ID: 9ihx

Title

Co-crystal structure of GH57 family amylopullulanase wild type from Aquifex aeolicus with maltopentaose

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus / complex / mutant

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 / alpha-maltotriose / Glycoside hydrolase family 57 N-terminal domain-containing protein

Function and homology information

Biological species

Aquifex aeolicus VF5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.86 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 18, 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	9ihx.cif.gz	417.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9ihx.ent.gz	343.1 KB	Display	PDB format
PDBx/mmJSON format	9ihx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ihx_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9ihx_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9ihx_validation.xml.gz	46.7 KB	Display
Data in CIF	9ihx_validation.cif.gz	63.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/9ihx ftp://data.pdbj.org/pub/pdb/validation_reports/ih/9ihx	HTTPS FTP

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Related structure data

Related structure data	8zyiC 9ihtC 9ihuC 9ihvC 9ihwC 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
57.8 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
57.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.533, 41.189, 195.083
Angle α, β, γ (deg.)	90.00, 96.12, 90.00
Int Tables number	3
Space group name H-M	P121

#1: Protein

Glycoside hydrolase family 57 N-terminal domain-containing protein

Mass: 57253.234 Da / Num. of mol.: 2 / Mutation: E256Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aquifex aeolicus 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

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.15 Å³/Da / Density % sol: 42.7 %
Crystal grow	Temperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium citrate, pH 4.2, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.86→96.99 Å / Num. obs: 81058 / % possible obs: 98 % / Redundancy: 6.3 % / CC_1/2: 0.988 / R_merge(I) obs: 0.24 / R_pim(I) all: 0.103 / R_rim(I) all: 0.262 / Χ²: 0.91 / Net I/σ(I): 5.1 / Num. measured all: 513051
Reflection shell	Resolution: 1.86→1.96 Å / % possible obs: 100 % / Redundancy: 6.2 % / R_merge(I) obs: 1.841 / Num. measured all: 74755 / Num. unique obs: 11976 / CC_1/2: 0.487 / R_pim(I) all: 0.8 / R_rim(I) all: 2.011 / Χ²: 0.84 / Net I/σ(I) obs: 1.2

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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: 1.86→61.183 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2249	3945	4.88 %
R_work	0.1779	-	-
obs	0.1802	80867	97.73 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.86→61.183 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8088	0	80	540	8708

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8396
X-RAY DIFFRACTION	f_angle_d	0.864	11362
X-RAY DIFFRACTION	f_dihedral_angle_d	5.96	5002
X-RAY DIFFRACTION	f_chiral_restr	0.051	1198
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 (%)
1.86-1.8824	0.3567	126	0.2994	2712	X-RAY DIFFRACTION	98
1.8824-1.9062	0.3934	153	0.2902	2725	X-RAY DIFFRACTION	98
1.9062-1.9313	0.3115	125	0.279	2777	X-RAY DIFFRACTION	99
1.9313-1.9578	0.3033	130	0.2647	2801	X-RAY DIFFRACTION	99
1.9578-1.9857	0.3218	125	0.2401	2780	X-RAY DIFFRACTION	100
1.9857-2.0154	0.2931	132	0.2239	2786	X-RAY DIFFRACTION	100
2.0154-2.0469	0.2826	130	0.2183	2844	X-RAY DIFFRACTION	100
2.0469-2.0804	0.2864	113	0.2184	2735	X-RAY DIFFRACTION	100
2.0804-2.1163	0.2434	151	0.2101	2808	X-RAY DIFFRACTION	100
2.1163-2.1548	0.2583	140	0.2034	2797	X-RAY DIFFRACTION	100
2.1548-2.1962	0.2523	142	0.2013	2816	X-RAY DIFFRACTION	100
2.1962-2.2411	0.2682	145	0.1974	2768	X-RAY DIFFRACTION	100
2.2411-2.2898	0.2734	143	0.1996	2299	X-RAY DIFFRACTION	83
2.2898-2.3431	0.2179	144	0.1826	2752	X-RAY DIFFRACTION	100
2.3431-2.4017	0.2525	163	0.1838	2820	X-RAY DIFFRACTION	100
2.4017-2.4666	0.2597	152	0.1818	2793	X-RAY DIFFRACTION	100
2.4666-2.5392	0.2694	144	0.1803	2767	X-RAY DIFFRACTION	100
2.5392-2.6211	0.2386	134	0.1786	2806	X-RAY DIFFRACTION	100
2.6211-2.7148	0.226	122	0.1907	2120	X-RAY DIFFRACTION	75
2.7148-2.8235	0.2104	152	0.1664	2802	X-RAY DIFFRACTION	100
2.8235-2.952	0.2376	142	0.1607	2856	X-RAY DIFFRACTION	100
2.952-3.1076	0.2216	157	0.1633	2780	X-RAY DIFFRACTION	100
3.1076-3.3023	0.2002	144	0.1597	2798	X-RAY DIFFRACTION	100
3.3023-3.5573	0.194	168	0.1548	2808	X-RAY DIFFRACTION	100
3.5573-3.9152	0.1568	127	0.1415	2435	X-RAY DIFFRACTION	85
3.9152-4.4816	0.1651	163	0.1325	2850	X-RAY DIFFRACTION	100
4.4816-5.6457	0.1961	134	0.145	2892	X-RAY DIFFRACTION	100
5.6457-61.183	0.1914	144	0.1754	2995	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	1.2355	-0.1446	-0.1363	0.311	0.1961	0.5251	-0.0395	-0.0987	-0.1078	0.0256	0.0244	0.0418	0.0624	-0.0929	0.0263	0.0905	-0.0118	0.0128	0.1205	0.0066	0.1398	-12.8969	14.9903	74.3682
2	2.5426	-0.0241	-1.3057	1.9018	0.0537	4.07	0.0839	-0.1253	0.3504	0.0342	-0.0471	0.0968	-0.4697	-0.0862	-0.0319	0.1222	-0.0012	0.0301	0.1659	-0.0173	0.2222	-25.5128	28.5419	81.3915
3	0.6827	-0.082	-0.1655	0.187	-0.0338	0.6927	-0.0005	0.0351	-0.0632	-0.0476	-0.005	-0.0233	0.0488	0.0812	0.0138	0.1241	-0.0046	0.0172	0.1198	-0.012	0.1748	1.8321	14.5321	66.7492
4	2.539	-0.1971	-1.0008	1.6172	0.3388	3.5332	0.0442	0.2943	0.0028	-0.2024	0.0118	0.0733	-0.1053	-0.0429	-0.0783	0.1117	-0.0242	-0.0149	0.1086	0.001	0.1238	-7.9972	23.5088	52.8425
5	0.8075	-0.0565	0.0802	0.8361	0.0693	4.2961	-0.0152	-0.0959	0.0496	0.0007	-0.0159	-0.003	-0.2309	0.18	-0.0046	0.0421	-0.0047	0.0155	0.139	-0.0064	0.1769	11.9846	21.1352	76.0636
6	5.1851	-1.7281	-0.0396	3.5237	-0.183	4.3075	-0.0259	-0.3587	0.1369	0.0995	0.0546	0.0327	0.008	0.0188	-0.0013	0.054	-0.0161	0.0095	0.1852	-0.0265	0.1092	1.899	17.4724	86.5001
7	1.2586	0.2501	-0.4726	0.1336	0.0516	1.0645	-0.0326	0.127	-0.1028	-0.0745	-0.0007	-0.0053	0.1461	0.2047	0.0459	0.2428	0.0481	-0.0127	0.1502	-0.0149	0.1327	-24.4594	34.904	22.0523
8	4.2189	0.0636	-1.4512	2.4784	-0.1674	4.7355	0.2032	0.2738	0.5436	-0.0998	-0.0267	0.1889	-0.514	-0.1011	-0.1655	0.3029	0.019	0.0106	0.1794	0.0617	0.2093	-16.9805	51.8442	9.4637
9	1.9014	1.0294	-1.7007	1.668	-1.3672	3.4659	-0.0566	-0.0709	-0.0764	-0.0712	-0.0855	-0.1532	0.1535	0.5243	0.1741	0.2006	0.0521	-0.0322	0.2126	-0.0199	0.1383	-11.1386	38.0181	18.7896
10	2.7378	-0.6417	-0.2274	1.1031	-0.1911	2.0178	0.0109	0.0578	-0.152	-0.0199	0.0367	0.1273	0.2435	-0.2169	-0.0501	0.2159	-0.0282	-0.0188	0.1003	-0.0063	0.1447	-44.4117	31.1395	29.9515
11	2.172	1.747	-0.8584	1.8989	-1.0103	2.0009	0.0471	-0.1144	0.0765	0.0236	-0.081	0.0871	-0.292	-0.1365	0.0118	0.2156	0.0695	-0.0086	0.1083	-0.0326	0.1691	-39.6576	44.1243	41.892
12	2.3581	0.7953	-1.5346	2.1106	-0.8037	4.8067	0.1018	-0.2372	0.1395	0.1463	-0.1242	0.0442	-0.48	0.142	0.0297	0.1768	0.0291	-0.0273	0.0999	-0.0154	0.1352	-28.0592	47.9211	42.6313
13	2.6812	0.0307	-1.1106	0.81	0.0668	4.0513	0.1656	-0.2758	0.0726	0.3716	-0.0943	-0.0162	-0.3487	0.2367	-0.0559	0.1909	0.0207	-0.0415	0.1292	-0.0269	0.1291	-24.0289	40.0556	45.181
14	1.1414	-0.0253	0.4092	1.5794	-0.359	5.5361	-0.0155	0.203	0.1046	-0.1574	0.0129	0.1223	-0.3251	-0.3994	0.031	0.1116	0.0147	-0.0299	0.165	0.0198	0.1934	-49.4659	41.1299	24.2217
15	5.6147	1.1636	0.2704	1.8512	0.021	4.1849	-0.1329	0.5308	0.1445	-0.1953	0.2264	0.0652	0.2662	-0.1041	-0.0022	0.2421	0.0224	-0.0319	0.2512	0.0175	0.0949	-41.0216	37.0903	12.4404

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 88 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 89 through 123 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 124 through 185 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 186 through 278 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 279 through 322 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 323 through 360 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 361 through 396 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 397 through 435 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 436 through 477 )

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