PDB-9iht: Crystal structure of GH57 family amylopullulanase from Aquifex ae...

ID or keywords:

Entry

Database: PDB / ID: 9iht

Title

Crystal structure of GH57 family amylopullulanase from Aquifex aeolicus in complex with acarbose

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus / 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 VF5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.692 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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Download

PDBx/mmCIF format	9iht.cif.gz	419.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9iht.ent.gz	345.7 KB	Display	PDB format
PDBx/mmJSON format	9iht.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9iht_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9iht_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9iht_validation.xml.gz	45.7 KB	Display
Data in CIF	9iht_validation.cif.gz	62.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/9iht ftp://data.pdbj.org/pub/pdb/validation_reports/ih/9iht	HTTPS FTP

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Related structure data

Related structure data	8zyiC 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 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 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.931, 40.109, 195.144
Angle α, β, γ (deg.)	90.00, 95.80, 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 VF5 (bacteria) / Gene: aq_720 / Production host:

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

#2: Polysaccharide

4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...

Type: oligosaccharide / Mass: 645.606 Da / Num. of mol.: 2 / Source method: obtained synthetically

Descriptor	Type	Program
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}	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.: 485 / 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: 2.07 Å³/Da / Density % sol: 40.63 %
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: BL10U2 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 23, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.69→97.07 Å / Num. obs: 105855 / % possible obs: 100 % / Redundancy: 5.2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.052 / R_rim(I) all: 0.124 / Χ²: 0.88 / Net I/σ(I): 9.2 / Num. measured all: 550396
Reflection shell	Resolution: 1.69→1.78 Å / % possible obs: 100 % / Redundancy: 4.6 % / R_merge(I) obs: 1.58 / Num. measured all: 71034 / Num. unique obs: 15318 / CC_1/2: 0.47 / R_pim(I) all: 0.78 / R_rim(I) all: 1.768 / Χ²: 0.73 / Net I/σ(I) obs: 1.4

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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: 1.692→60.619 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2002	5113	4.86 %
R_work	0.1709	-	-
obs	0.1723	105119	99.29 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.692→60.619 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8188	0	0	485	8673

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8469
X-RAY DIFFRACTION	f_angle_d	0.95	11465
X-RAY DIFFRACTION	f_dihedral_angle_d	5.862	7082
X-RAY DIFFRACTION	f_chiral_restr	0.056	1209
X-RAY DIFFRACTION	f_plane_restr	0.006	1436

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 (%)
1.692-1.7109	0.3379	155	0.302	2962	X-RAY DIFFRACTION	90
1.7109-1.7311	0.3214	159	0.2958	3185	X-RAY DIFFRACTION	94
1.7311-1.7522	0.2983	168	0.2758	3199	X-RAY DIFFRACTION	97
1.7522-1.7743	0.3117	177	0.274	3263	X-RAY DIFFRACTION	99
1.7743-1.7977	0.3018	183	0.2646	3316	X-RAY DIFFRACTION	100
1.7977-1.8223	0.27	184	0.2338	3369	X-RAY DIFFRACTION	100
1.8223-1.8484	0.3029	163	0.2243	3269	X-RAY DIFFRACTION	100
1.8484-1.876	0.2586	184	0.2105	3309	X-RAY DIFFRACTION	100
1.876-1.9053	0.2465	172	0.1962	3383	X-RAY DIFFRACTION	100
1.9053-1.9365	0.2228	162	0.1952	3273	X-RAY DIFFRACTION	100
1.9365-1.9699	0.2391	179	0.1862	3378	X-RAY DIFFRACTION	100
1.9699-2.0057	0.2088	180	0.1818	3309	X-RAY DIFFRACTION	100
2.0057-2.0443	0.1927	181	0.174	3292	X-RAY DIFFRACTION	100
2.0443-2.086	0.2204	161	0.1807	3374	X-RAY DIFFRACTION	100
2.086-2.1314	0.1998	172	0.1632	3309	X-RAY DIFFRACTION	100
2.1314-2.181	0.1882	181	0.1608	3342	X-RAY DIFFRACTION	100
2.181-2.2355	0.1883	173	0.1575	3362	X-RAY DIFFRACTION	100
2.2355-2.296	0.1916	177	0.1572	3320	X-RAY DIFFRACTION	100
2.296-2.3635	0.2055	183	0.1626	3381	X-RAY DIFFRACTION	100
2.3635-2.4398	0.1812	153	0.1675	3338	X-RAY DIFFRACTION	100
2.4398-2.527	0.1981	173	0.1608	3382	X-RAY DIFFRACTION	100
2.527-2.6282	0.2125	171	0.1593	3326	X-RAY DIFFRACTION	100
2.6282-2.7478	0.1957	149	0.1599	3362	X-RAY DIFFRACTION	100
2.7478-2.8927	0.1965	146	0.1596	3443	X-RAY DIFFRACTION	100
2.8927-3.0739	0.2039	173	0.1562	3372	X-RAY DIFFRACTION	100
3.0739-3.3112	0.1798	184	0.1542	3362	X-RAY DIFFRACTION	100
3.3112-3.6444	0.1726	158	0.1462	3440	X-RAY DIFFRACTION	100
3.6444-4.1717	0.1595	182	0.1356	3352	X-RAY DIFFRACTION	100
4.1717-5.2554	0.1525	186	0.1463	3441	X-RAY DIFFRACTION	100
5.2554-60.619	0.1768	144	0.1795	3593	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	1.3651	0.1273	-0.5371	0.6219	0.2408	1.9946	0.3244	-0.4654	-0.0854	0.339	-0.2113	-0.1367	-0.0107	0.2003	-0.1417	0.2187	-0.0948	-0.0469	0.1705	0.0108	0.1347	-23.301	35.4584	45.0041
2	1.5012	0.0987	0.2398	1.3643	0.0284	2.4399	0.103	0.321	0.2868	-0.104	-0.1179	0.244	-0.074	-0.5218	0.0623	0.0894	-0.012	0.0183	0.2674	0.0308	0.1902	-48.7254	35.3819	24.199
3	3.3212	0.6459	-0.0749	2.6512	-0.0458	3.5261	-0.0679	0.5516	0.0288	-0.2849	0.0604	0.216	0.0637	-0.0961	-0.042	0.1252	-0.0016	-0.0284	0.2829	-0.009	0.1204	-40.4591	30.3946	12.7615
4	1.014	0.1581	-0.1398	0.5319	0.1543	0.8155	-0.0793	0.021	-0.0495	-0.1031	0.0849	0.0745	0.0193	0.0038	0.0133	0.0882	-0.0432	-0.0076	0.0843	0.0156	0.0967	-10.063	11.982	69.0881
5	2.0481	-1.1855	-1.8388	1.0409	1.2855	1.9412	-0.1769	-0.2206	-0.1925	0.1334	0.0276	0.1433	0.2014	-0.1297	0.0707	0.1344	-0.0035	0.0004	0.1717	0.0231	0.128	-17.1597	9.7033	85.4903
6	1.4197	-0.1999	-1.0917	0.9661	0.4369	1.7918	0.0569	-0.0005	0.1599	0.0315	-0.0271	0.1166	-0.1222	-0.1556	-0.0049	0.0809	-0.0087	-0.0213	0.1264	0.0197	0.1413	-24.146	19.6894	79.024
7	0.965	0.0356	0.2287	0.601	-0.1701	0.8791	-0.1157	0.137	-0.0353	-0.1708	0.1083	-0.0533	0.0039	0.1043	0.0155	0.1543	-0.0748	0.0167	0.11	-0.011	0.1103	4.4241	14.3524	63.176
8	1.5976	-0.1113	-0.3509	0.8837	-0.1347	2.0702	-0.0468	0.3103	0.0035	-0.3024	0.1017	-0.0404	-0.0412	-0.0646	-0.046	0.2166	-0.1051	-0.055	0.1661	0.0192	0.1223	-9.5837	15.4972	51.6688
9	1.4234	0.0463	0.0784	1.1958	-0.0605	2.3121	-0.1161	-0.0754	0.1107	-0.0275	0.0482	-0.0764	-0.2216	0.1221	0.0177	0.0631	-0.0367	-0.0041	0.1324	-0.0027	0.1372	12.3285	17.6697	76.2499
10	3.6702	-0.26	-0.1734	2.4506	-0.0913	3.3065	-0.1256	-0.2917	0.1343	0.0703	0.0363	-0.0097	-0.0981	-0.1177	0.0592	0.0458	-0.0005	-0.0156	0.1735	-0.004	0.086	2.1938	13.8947	86.764
11	1.5439	0.4165	-0.2726	0.9493	0.0211	1.0304	0.0795	0.0927	-0.178	0.0536	-0.0684	-0.0887	0.2216	0.0153	-0.0323	0.1016	0.01	-0.0141	0.0645	-0.0171	0.1107	-25.3728	30.2412	28.0727
12	1.3056	0.4448	-1.4991	0.4045	-0.9493	2.5568	-0.1503	0.6672	-0.4047	-0.227	-0.065	-0.106	0.5094	0.0749	0.0478	0.1933	0.0187	-0.0043	0.3386	-0.1049	0.185	-21.1486	26.2903	10.9217
13	1.641	0.0452	-0.6445	1.2034	0.4684	3.0417	0.0704	0.4448	0.1828	-0.1432	-0.0327	-0.0953	-0.3488	0.282	-0.1185	0.1408	0.0075	0.0207	0.2719	0.0212	0.1706	-12.4254	41.2836	12.1046
14	1.2973	0.387	-0.2801	0.6763	-0.1368	1.4441	-0.0003	0.174	-0.2536	0.0525	0.0312	0.0014	0.2293	-0.1054	-0.0226	0.1686	-0.0071	-0.0315	0.0562	-0.0434	0.1448	-32.9162	28.1413	25.0988
15	1.5149	-0.3352	-0.3541	1.4868	0.0716	1.6857	0.0047	0.0582	-0.4598	0.1973	-0.026	-0.1579	0.4684	-0.2577	-0.017	0.2289	-0.0746	0.0072	0.1147	-0.0126	0.2303	-41.3224	22.5523	33.7412
16	1.6253	1.3687	0.1415	1.6303	-0.5228	1.0433	0.1644	-0.2812	0.3006	0.1243	-0.1324	0.0962	-0.1323	-0.2196	-0.0704	0.2192	-0.0343	0.0858	0.0987	-0.0501	0.2292	-38.5356	39.9957	41.416
17	1.0746	0.4135	-0.4377	0.9451	-0.1055	1.0341	0.4285	-0.3514	0.4508	0.3802	-0.2601	0.0473	-0.3621	0.087	-0.1086	0.3038	-0.1269	0.072	0.1463	-0.1097	0.1937	-27.2112	43.2824	42.0946

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 361 through 396 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 397 through 435 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 436 through 477 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 2 through 57 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 58 through 88 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 89 through 185 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 186 through 360 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 361 through 396 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 397 through 435 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 436 through 477 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2 through 57 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 88 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 89 through 158 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 159 through 226 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 227 through 278 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 279 through 322 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 323 through 360 )

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