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

ID or keywords:

Entry

Database: PDB / ID: 9jls

Title

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

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus

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-acarbose / 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: 3.06 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

1items

Citation

Journal: Cryst.Growth Des. / Year: 2024
Title: High-Temperature Crystallization Method for the GH57 Family Hyperthermophilic Amylopullulanase from Aquifex aeolicus
Authors: Zhu, Z. / Wang, W. / Huang, L. / Xu, Q. / Zhou, H. / Li, M. / Yu, F. / Wang, Q.

History

Deposition	Sep 19, 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	9jls.cif.gz	811.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9jls.ent.gz	680.6 KB	Display	PDB format
PDBx/mmJSON format	9jls.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jl/9jls ftp://data.pdbj.org/pub/pdb/validation_reports/jl/9jls	HTTPS FTP

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Related structure data

Related structure data	9jlqC 9jlrC 9jlwC 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	#138 - Jun 2011 Glucansucrase similarity (1) #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

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

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

hetero molecules

235 kDa, 4 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
58.8 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
58.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

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

hetero molecules

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

4

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.430, 167.410, 97.980
Angle α, β, γ (deg.)	90.00, 109.38, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Glycoside hydrolase family 57 N-terminal domain-containing protein

Mass: 58186.254 Da / Num. of mol.: 4
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, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose

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

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: 2.43 Å³/Da / Density % sol: 49.32 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 40% MPD, 5% PEG 8000, 0.1M MES 6.5

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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: Aug 1, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 3.06→66.5 Å / Num. obs: 41253 / % possible obs: 99.4 % / Redundancy: 5.8 % / CC_1/2: 0.961 / R_rim(I) all: 0.406 / Net I/σ(I): 4.5
Reflection shell	Resolution: 3.06→3.14 Å / R_merge(I) obs: 1.653 / Num. unique obs: 3050 / CC_1/2: 0.357 / R_pim(I) all: 0.761 / R_rim(I) all: 1.824

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.06→66.5 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2296	2058	5 %
R_work	0.1802	-	-
obs	0.1826	41196	99.19 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.06→66.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16342	0	176	0	16518

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	16984
X-RAY DIFFRACTION	f_angle_d	0.529	22984
X-RAY DIFFRACTION	f_dihedral_angle_d	6.649	2226
X-RAY DIFFRACTION	f_chiral_restr	0.042	2428
X-RAY DIFFRACTION	f_plane_restr	0.004	2882

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 (%)
3.06-3.13	0.3597	127	0.292	2616	X-RAY DIFFRACTION	99
3.13-3.21	0.3255	115	0.2597	2597	X-RAY DIFFRACTION	99
3.21-3.3	0.31	147	0.2467	2604	X-RAY DIFFRACTION	99
3.3-3.39	0.2789	133	0.2253	2599	X-RAY DIFFRACTION	100
3.39-3.5	0.2715	148	0.2246	2591	X-RAY DIFFRACTION	99
3.5-3.63	0.2582	140	0.1992	2612	X-RAY DIFFRACTION	99
3.63-3.77	0.2347	142	0.1911	2585	X-RAY DIFFRACTION	100
3.77-3.94	0.2247	164	0.179	2557	X-RAY DIFFRACTION	99
3.94-4.15	0.2399	132	0.1641	2615	X-RAY DIFFRACTION	99
4.15-4.41	0.2003	155	0.1545	2617	X-RAY DIFFRACTION	99
4.41-4.75	0.1929	136	0.1496	2608	X-RAY DIFFRACTION	99
4.75-5.23	0.2167	124	0.1509	2643	X-RAY DIFFRACTION	99
5.23-5.99	0.2631	110	0.1744	2645	X-RAY DIFFRACTION	100
5.99-7.54	0.2105	140	0.1842	2632	X-RAY DIFFRACTION	100
7.54-66.5	0.1554	145	0.1354	2617	X-RAY DIFFRACTION	98

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	3.5471	0.692	-0.3766	0.867	0.3828	1.3599	-0.109	-0.0474	-0.189	0.0447	0.1491	-0.1317	0.175	0.1658	-0.0604	0.3283	0.0391	-0.0233	0.4097	-0.0012	0.3931	19.4554	-3.439	9.5792
2	7.4754	2.6213	0.5648	4.2449	-0.0138	0.9745	-0.0382	-0.2842	0.2024	0.0542	0.0275	-0.2553	0.0953	0.0775	0.0227	0.3394	0.0118	-0.0121	0.3977	-0.0351	0.2764	31.414	4.5891	15.024
3	2.0376	0.1502	-0.2887	2.0877	-0.0853	0.9474	0.0131	0.067	0.0538	-0.1033	-0.0082	0.2012	0.0459	-0.219	-0.0071	0.3041	-0.0201	-0.0364	0.3008	0.0084	0.3117	0.9077	0.2222	1.9624
4	5.7047	2.2654	2.966	7.1344	2.2748	7.8529	0.0897	-0.2474	0.0562	0.2757	-0.3281	0.2631	0.4255	-0.4704	0.2128	0.3708	-0.0106	0.0185	0.2886	0.0105	0.2633	0.2942	4.6911	19.6419
5	8.5735	-0.9563	-5.0983	2.5529	1.0133	4.7939	-0.0737	0.989	0.1633	-0.3166	-0.0652	0.0095	-0.059	-0.4616	0.1097	0.5054	-0.0952	-0.0805	0.4111	0.0077	0.2726	6.5238	0.5255	-12.4336
6	9.3078	-1.3338	-0.7209	4.926	0.5515	6.7743	-0.0208	0.3283	0.5017	0.091	0.3733	-0.3878	-0.4699	0.3871	-0.4159	0.4291	-0.0686	0.023	0.4777	-0.0013	0.2662	20.8734	-4.0231	-10.0625
7	3.8333	0.2684	0.0705	0.5734	-0.0463	1.1922	0.0095	-0.2543	0.0687	0.0845	-0.0117	0.1935	0.0193	-0.1612	0.0053	0.351	-0.0091	0.0339	0.3336	-0.0223	0.421	-24.701	39.0243	30.0854
8	1.5339	-0.3315	-0.9484	4.1525	2.3985	4.0902	0.0113	0.3205	0.0464	-0.7197	0.0129	-0.0985	-0.3087	0.0132	-0.0991	0.4834	-0.0646	0.041	0.4727	0.1008	0.4143	-5.3973	46.3716	8.2107
9	2.1823	1.5165	-0.039	4.7639	-0.9635	1.4542	-0.1001	0.2224	-0.0849	-0.3573	0.1441	-0.1041	0.0266	0.1679	-0.0029	0.3346	0.0161	0.0954	0.4223	-0.0241	0.3451	3.1415	38.2706	19.9715
10	5.5318	1.0451	0.4678	4.011	0.4044	3.7398	0.1367	-0.4805	-0.5201	0.4323	-0.0572	-0.1852	0.2629	-0.0401	-0.0809	0.3843	0.0073	0.0176	0.389	-0.0196	0.2652	-0.4828	31.5924	34.7792
11	3.3369	-0.3796	1.8707	2.2522	-0.7758	3.3366	-0.1586	0.4377	-0.4117	-0.255	0.1199	0.2518	-0.0424	0.0497	0.0511	0.4991	-0.1171	0.0548	0.5506	-0.0083	0.3137	-6.1306	37.4966	5.2712
12	7.0605	-3.0676	0.8336	7.1937	1.3877	4.1388	-0.0526	0.5761	-0.3693	0.3732	-0.2512	0.8366	0.3358	0.1132	0.2824	0.5032	-0.072	-0.0236	0.4894	-0.0198	0.3573	-20.3317	42.0526	7.2509
13	2.1657	1.1124	-0.4544	3.0825	0.3525	1.7474	-0.186	0.2286	0.1235	-0.2675	0.2478	-0.0875	-0.2618	0.1507	-0.065	0.4582	-0.0093	0.0659	0.503	0.0462	0.3778	29.0943	49.3303	-25.5219
14	7.1555	6.1726	1.6353	9.6063	-1.8759	2.9143	-0.1221	0.2035	0.1037	0.6395	0.1974	-1.2794	0.6096	0.8108	-0.0706	0.6121	0.1781	0.0698	0.8742	-0.2286	0.7579	50.9994	47.8303	-20.3762
15	1.7836	0.5743	-0.788	1.634	0.3068	2.6738	-0.0786	0.1059	0.0512	-0.0619	0.1326	-0.0958	0.0982	-0.0933	-0.039	0.4626	0.0327	0.0598	0.3937	0.0227	0.3664	21.9135	43.6511	-20.3642
16	9.0434	1.6922	0.2216	3.1975	1.0821	2.8463	0.064	0.4577	-0.7924	-0.1328	0.1367	-0.2969	0.7971	-0.0583	-0.1685	0.9119	-0.0025	0.0613	0.4847	0.0241	0.3527	21.8945	27.3665	-27.7058
17	3.3322	2.1771	0.8277	8.9673	2.2623	4.1116	0.1486	-0.1567	-0.1772	0.9359	-0.2589	-0.7005	0.373	-0.1902	0.1108	0.4237	0.0118	0.0826	0.4102	0.1091	0.3454	18.5954	44.4109	-2.5468
18	6.1372	1.9849	-2.2741	4.6428	2.7022	4.1275	-0.341	-0.2685	-0.7228	-0.6275	0.3325	-0.8213	0.2532	0.8136	0.0846	0.3665	-0.0333	0.1704	0.69	0.085	0.4102	26.5923	52.4877	-7.4301
19	5.7434	-5.3019	-1.4948	8.4305	1.1529	2.2936	-0.1369	-0.3708	0.2589	0.3607	0.0302	-0.669	-0.2811	0.4811	0.1477	0.5101	-0.0378	-0.0712	0.5199	0.1066	0.3562	25.7452	66.1583	-6.6979
20	1.8439	0.7613	-0.1544	2.0864	-0.8658	1.7311	-0.1062	0.4328	0.1369	-0.1503	0.2319	0.4207	0.0178	-0.3409	-0.1386	0.4646	-0.0752	-0.0779	0.6092	-0.0043	0.4511	4.6451	-10.7294	47.5581
21	2.8196	0.482	0.1341	2.5517	0.0517	4.8859	0.096	0.1119	0.0952	0.2271	-0.1241	-0.283	-0.0498	0.3489	0.038	0.353	0.0102	-0.0326	0.3768	0.0066	0.3896	29.0279	-8.915	63.9163
22	1.8798	0.093	0.4189	1.6973	-0.8094	3.8288	-0.0909	0.2699	0.4253	-0.1595	0.0508	0.1539	-0.6385	0.0427	0.0366	0.4739	0.0164	-0.0163	0.4056	-0.0286	0.429	21.692	5.7768	56.2175
23	5.9269	5.6921	1.6711	5.896	-0.2954	9.043	0.0249	-0.1639	0.9894	-1.1816	-0.0606	0.5833	-1.5447	-0.0467	0.095	0.6421	-0.0748	-0.103	0.469	0.0288	0.324	13.0773	-13.6726	67.4478
24	2.9322	-0.2316	1.48	3.6934	-0.7652	1.5513	-0.1886	-0.1852	-0.0409	-0.1562	0.065	0.1157	0.0939	-0.3509	0.1265	0.4982	-0.0689	-0.0039	0.5708	-0.0689	0.4912	13.6158	-27.1305	68.5684

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 88 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 185 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 186 through 360 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 361 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 1 through 194 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 195 through 245 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 246 through 322 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 323 through 396 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 397 through 435 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 436 through 477 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 88 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 89 through 123 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 124 through 322 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 323 through 396 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 397 through 435 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 436 through 460 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 461 through 484 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1 through 200 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 201 through 278 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 279 through 435 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 436 through 460 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 461 through 484 )

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