PDB-9ihu: GH57 family Amylopullulanase from Aquifex aeolicus

ID or keywords:

Entry

Database: PDB / ID: 9ihu

Title

GH57 family Amylopullulanase from Aquifex aeolicus

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / Amylopullulanase / Aquifex aeolicus / GH57 family

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: 1.79 Å

Authors

Zhu, Z.M. / Wang, W.W. / Li, M.J. / Xu, Q. / Zhou, H. / Huang, L.Q. / Wang, Q.S. / 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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Download

PDBx/mmCIF format	9ihu.cif.gz	407 KB	Display	PDBx/mmCIF format
PDB format	pdb9ihu.ent.gz	333.6 KB	Display	PDB format
PDBx/mmJSON format	9ihu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ihu_validation.pdf.gz	436.3 KB	Display	wwPDB validaton report
Full document	9ihu_full_validation.pdf.gz	446 KB	Display
Data in XML	9ihu_validation.xml.gz	46.1 KB	Display
Data in CIF	9ihu_validation.cif.gz	63.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/9ihu ftp://data.pdbj.org/pub/pdb/validation_reports/ih/9ihu	HTTPS FTP

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Related structure data

Related structure data	8zyiC 9ihtC 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

115 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

defined by author
Evidence: gel filtration
57.3 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

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

Unit cell

Length a, b, c (Å)	61.441, 40.918, 194.064
Angle α, β, γ (deg.)	90.00, 95.91, 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 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H₂O
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: 2.12 Å³/Da / Density % sol: 41.96 %
Crystal grow	Temperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium citrate, pH 4.6, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.79→193.03 Å / Num. obs: 91529 / % possible obs: 100 % / Redundancy: 6.2 % / CC_1/2: 0.983 / R_merge(I) obs: 0.153 / R_pim(I) all: 0.067 / R_rim(I) all: 0.168 / Χ²: 0.73 / Net I/σ(I): 6.4 / Num. measured all: 565908
Reflection shell	Resolution: 1.79→1.84 Å / % possible obs: 100 % / Redundancy: 5.3 % / R_merge(I) obs: 0.713 / Num. measured all: 35343 / Num. unique obs: 6696 / CC_1/2: 0.687 / R_pim(I) all: 0.344 / R_rim(I) all: 0.795 / Χ²: 0.44 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
Aimless		data scaling
xia2		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.79→38.606 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.84 / Phase error: 23.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2249	4538	4.98 %
R_work	0.1906	-	-
obs	0.1923	91171	99.6 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.79→38.606 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8104	0	0	560	8664

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8330
X-RAY DIFFRACTION	f_angle_d	0.821	11266
X-RAY DIFFRACTION	f_dihedral_angle_d	2.9	4968
X-RAY DIFFRACTION	f_chiral_restr	0.051	1170
X-RAY DIFFRACTION	f_plane_restr	0.006	1426

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 (%)
1.79-1.8103	0.3083	128	0.261	2911	X-RAY DIFFRACTION	100
1.8103-1.8316	0.3007	151	0.2523	2864	X-RAY DIFFRACTION	100
1.8316-1.854	0.3198	152	0.2562	2918	X-RAY DIFFRACTION	100
1.854-1.8775	0.3223	135	0.2755	2833	X-RAY DIFFRACTION	100
1.8775-1.9022	0.3776	137	0.3384	2863	X-RAY DIFFRACTION	99
1.9022-1.9282	0.3506	151	0.2954	2859	X-RAY DIFFRACTION	99
1.9282-1.9558	0.3858	136	0.3717	2676	X-RAY DIFFRACTION	93
1.9558-1.9849	0.3382	133	0.2583	2870	X-RAY DIFFRACTION	100
1.9849-2.016	0.2749	154	0.2045	2858	X-RAY DIFFRACTION	100
2.016-2.049	0.258	183	0.1932	2943	X-RAY DIFFRACTION	100
2.049-2.0843	0.2388	165	0.1894	2748	X-RAY DIFFRACTION	100
2.0843-2.1222	0.2272	139	0.1787	2952	X-RAY DIFFRACTION	100
2.1222-2.1631	0.224	140	0.1775	2862	X-RAY DIFFRACTION	100
2.1631-2.2072	0.2248	149	0.1725	2842	X-RAY DIFFRACTION	100
2.2072-2.2552	0.228	156	0.1745	2897	X-RAY DIFFRACTION	100
2.2552-2.3076	0.2338	141	0.1826	2905	X-RAY DIFFRACTION	100
2.3076-2.3653	0.2438	150	0.191	2887	X-RAY DIFFRACTION	100
2.3653-2.4293	0.1988	138	0.1922	2887	X-RAY DIFFRACTION	100
2.4293-2.5008	0.2455	156	0.1804	2853	X-RAY DIFFRACTION	100
2.5008-2.5815	0.2407	139	0.1777	2936	X-RAY DIFFRACTION	100
2.5815-2.6737	0.226	175	0.1748	2863	X-RAY DIFFRACTION	100
2.6737-2.7807	0.1989	157	0.1749	2868	X-RAY DIFFRACTION	100
2.7807-2.9072	0.1943	160	0.176	2923	X-RAY DIFFRACTION	100
2.9072-3.0605	0.1882	135	0.1752	2920	X-RAY DIFFRACTION	100
3.0605-3.2521	0.1921	140	0.1802	2915	X-RAY DIFFRACTION	100
3.2521-3.5031	0.2063	158	0.165	2925	X-RAY DIFFRACTION	100
3.5031-3.8553	0.1764	169	0.1577	2908	X-RAY DIFFRACTION	100
3.8553-4.4125	0.1877	162	0.1484	2943	X-RAY DIFFRACTION	100
4.4125-5.5566	0.1826	163	0.1592	2954	X-RAY DIFFRACTION	100
5.5566-38.606	0.2117	186	0.1955	3050	X-RAY DIFFRACTION	99

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	0.0279	0.0145	-0.018	0.0145	0.0058	0.0203	0.0197	-0.026	-0.048	-0.0411	-0.0385	-0.0325	0.0746	0.0534	-0.0154	0.1416	0.0924	0.0055	0.0984	-0.094	-0.0857	4.7226	-3.5688	26.988
2	0.0015	0.0035	0.0007	0.0019	0.0011	0.0051	0.0035	0.0376	0.0291	-0.0085	0.013	0.0084	0.0334	0.007	0	0.2454	0.0521	-0.0263	0.3435	-0.0096	0.1195	11.1361	2.4049	5.5403
3	0.077	0.0042	0.0572	0.0149	0.0364	0.1087	-0.0515	0.0994	-0.0351	0.0322	0.0638	-0.0097	0.003	0.2388	-0.0315	0.1407	0.0867	-0.0001	0.2248	-0.0061	0.0747	17.9166	2.7336	18.2784
4	0.0144	0.0094	-0.0228	0.0461	-0.0389	0.0478	0.0163	0.0737	-0.0165	0.0068	0.0917	0.0211	0.1791	-0.1161	0.0059	0.1884	0.0134	-0.0383	0.1225	-0.0091	0.1179	-15.3414	-7.0098	28.7995
5	0.0035	0.0024	0.01	0.0142	-0.0259	0.0411	0.0389	-0.0339	-0.0125	-0.0362	-0.0042	0.0456	-0.0691	-0.1008	0.0016	0.1608	0.0255	0.0018	0.112	-0.0084	0.1218	-8.471	5.4074	41.5348
6	0.0052	-0.0046	0.0031	0.0033	0.0013	0.0067	0.0342	-0.0276	0.051	0.0059	-0.0465	0.0269	-0.0613	0.0079	-0.0056	0.1792	0.014	0.0005	0.1064	-0.0279	0.0822	3.247	9.6772	42.4003
7	0.0077	-0.0114	0.0027	0.01	-0.0052	0.0048	0.0059	-0.0315	0.0002	0.0252	0.0135	0.007	-0.0259	0.0326	-0	0.1346	-0.0031	-0.0188	0.1672	-0.0184	0.0884	7.1837	1.7154	45.0219
8	0.0091	0.0052	0.0026	0.0045	-0.0048	0.0051	0.0183	0.0523	0.0449	-0.0405	0.0009	0.0548	-0.0114	-0.0364	0	0.1433	0.0251	-0.0302	0.1936	0.0291	0.1329	-18.4675	3.0235	24.2263
9	0.0318	-0.0192	-0.0046	0.0116	0.0002	0.0021	-0.0172	0.0697	0.0443	-0.0001	-0.0096	-0.0187	0.0202	-0.0327	0.0013	0.1744	0.0141	-0.0364	0.1899	-0.0039	0.0789	-10.1117	-1.0782	12.1192
10	0.0719	-0.0109	0.0192	0.0351	0.0044	0.0549	-0.0302	-0.0128	-0.0445	-0.0046	-0.0003	0.018	0.0152	-0.0098	-0.0412	0.0296	-0.0179	-0.0037	0.0498	0.0016	0.0671	17.65	-21.0402	75.6978
11	0.0253	0.0294	-0.0245	0.0216	-0.0096	0.0308	-0.0144	0.048	0.0303	-0.0531	0.0451	0.0178	-0.0322	-0.0956	0.0044	0.02	-0.0287	0.0139	0.0296	-0.0086	0.1141	6.6806	-16.2697	75.402
12	0.0356	-0.0016	-0.0057	0.0066	-0.0161	0.0196	-0.002	0.096	-0.0613	-0.0429	-0.0189	-0.0234	0.0938	0.1639	-0.0031	0.0004	-0.1206	0.007	-0.1895	-0.0187	0.0939	38.9901	-22.0891	65.5361
13	0.0475	0.0205	-0.0189	0.0226	0.0018	0.0497	0.0075	0.1079	0.0238	-0.0647	0.0228	0.0517	-0.0262	-0.0209	0.0221	0.0839	-0.0178	0.0014	0.0967	0.0067	0.066	23.1252	-14.4727	52.5724
14	0.0363	0.012	0.007	0.0058	-0.0013	0.0066	-0.0003	-0.0184	0.0491	-0.0017	-0.0088	-0.0063	-0.0341	0.0187	0.0006	0.037	0.0008	0.0048	0.0744	-0.0077	0.1113	43.1567	-16.6658	75.7249
15	0.0172	0.0056	0.0082	0.0043	0.0044	0.0146	-0.0191	-0.0674	-0.0047	-0.0053	-0.0186	0.02	-0.0216	-0.0093	-0.0075	0.0014	0.0123	-0.0135	0.042	0.0204	0.0822	32.9392	-20.2274	86.431

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 194 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 195 through 273 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 274 through 322 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 323 through 360 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 361 through 396 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 397 through 435 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 436 through 477 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 102 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 103 through 194 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 195 through 322 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 323 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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