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

ID or keywords:

Entry

Database: PDB / ID: 9jlq

Title

Crystal structure of GH57 family amylopullulanase from Aquifex aeolicus wild type apo

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 / 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: 2.54 Å

Authors

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

Funding support

China, 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	9jlq.cif.gz	803.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9jlq.ent.gz	673.3 KB	Display	PDB format
PDBx/mmJSON format	9jlq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jlq_validation.pdf.gz	452.8 KB	Display	wwPDB validaton report
Full document	9jlq_full_validation.pdf.gz	484.7 KB	Display
Data in XML	9jlq_validation.xml.gz	72.2 KB	Display
Data in CIF	9jlq_validation.cif.gz	94.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jl/9jlq ftp://data.pdbj.org/pub/pdb/validation_reports/jl/9jlq	HTTPS FTP

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Related structure data

Related structure data	9jlrC 9jlsC 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	#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

233 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

defined by author
Evidence: gel filtration
58.2 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
58.2 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

defined by author
58.2 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

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

Unit cell

Length a, b, c (Å)	72.658, 166.730, 99.514
Angle α, β, γ (deg.)	90.00, 110.31, 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.43 Å³/Da / Density % sol: 49.36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 40% MPD, 5% PEG2W, 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: 0.97915 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 23, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.54→99.33 Å / Num. obs: 45539 / % possible obs: 88.4 % / Redundancy: 4.2 % / CC_1/2: 0.905 / Net I/σ(I): 3.7
Reflection shell	Resolution: 2.54→2.814 Å / R_merge(I) obs: 1.47 / Num. unique obs: 2275 / CC_1/2: 0.376 / R_pim(I) all: 0.792

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
XDS		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.54→93.33 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2426	2259	4.97 %
R_work	0.1979	-	-
obs	0.2002	45452	62.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.54→93.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16333	0	0	160	16493

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	16794
X-RAY DIFFRACTION	f_angle_d	0.61	22715
X-RAY DIFFRACTION	f_dihedral_angle_d	5.161	2118
X-RAY DIFFRACTION	f_chiral_restr	0.042	2355
X-RAY DIFFRACTION	f_plane_restr	0.005	2877

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 (%)
2.54-2.6	0.1036	2	0.2111	44	X-RAY DIFFRACTION	1
2.6-2.66	0.3374	17	0.2033	280	X-RAY DIFFRACTION	7
2.66-2.72	0.2832	36	0.2725	652	X-RAY DIFFRACTION	15
2.72-2.8	0.325	54	0.2719	937	X-RAY DIFFRACTION	22
2.8-2.88	0.3101	51	0.2459	1197	X-RAY DIFFRACTION	28
2.88-2.97	0.2962	88	0.2576	1608	X-RAY DIFFRACTION	38
2.97-3.08	0.2854	127	0.2457	2335	X-RAY DIFFRACTION	54
3.08-3.2	0.2979	127	0.2334	3005	X-RAY DIFFRACTION	69
3.2-3.35	0.2775	174	0.2383	3390	X-RAY DIFFRACTION	78
3.35-3.52	0.2737	208	0.2249	3998	X-RAY DIFFRACTION	92
3.52-3.74	0.2532	244	0.1958	4297	X-RAY DIFFRACTION	99
3.74-4.03	0.2624	222	0.1872	4320	X-RAY DIFFRACTION	99
4.03-4.44	0.2166	230	0.1669	4250	X-RAY DIFFRACTION	99
4.44-5.08	0.2011	198	0.1578	4278	X-RAY DIFFRACTION	98
5.08-6.4	0.2151	249	0.1914	4266	X-RAY DIFFRACTION	99
6.4-93.33	0.192	232	0.1791	4336	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	1.5797	0.7528	0.4848	0.8734	0.1438	0.865	-0.1107	0.1091	-0.2263	0.1707	0.1242	-0.2588	0.0831	0.2451	-0.0164	0.136	0.0324	-0.0838	0.075	0.0199	0.0674	17.6551	-3.7732	9.9113
2	3.3087	0.448	0.3747	1.5488	0.2954	1.2723	0.0463	0.0454	0.2415	0.1883	0.0948	-0.3264	0.0926	0.3416	-0.1122	0.1654	-0.0139	-0.0202	0.2094	-0.0578	0.2111	32.771	4.0212	15.0413
3	1.2628	0.3713	-0.2383	1.3799	0.2729	1.8191	-0.1256	0.1935	-0.0603	-0.1509	0.111	0.0685	0.1228	-0.0987	-0.0408	0.1371	-0.0299	-0.0067	0.098	-0.0152	0.1306	1.1451	-2.9773	-1.1334
4	3.0603	0.306	0.0653	1.9149	0.1874	2.2263	0.022	-0.2802	0.3941	0.0308	0.0222	0.2192	0.1091	-0.0961	-0.0223	0.116	-0.0061	-0.0348	0.1369	-0.037	0.0961	1.1111	8.1338	17.0331
5	1.0419	-0.9432	0.0983	2.5291	1.3616	1.3949	-0.0803	0.4231	0.3625	-0.7442	0.3125	-0.7148	-0.2755	0.0516	-0.0334	0.1989	-0.0547	-0.1515	0.2443	0.0157	0.0437	6.5447	1.1049	-11.9226
6	4.2133	0.4574	0.3333	3.5406	-0.2653	3.7414	-0.1818	0.26	0.3373	0.217	0.1577	-0.4843	-0.314	0.3737	-0.0427	0.1367	0.007	-0.0023	0.3204	-0.0382	0.2472	21.0609	-4.1533	-10.1928
7	2.7722	0.039	-0.0751	0.7757	-0.0546	0.6388	0.002	-0.418	-0.1121	0.0348	0.1053	0.2572	0.0151	-0.2395	-0.0608	0.1436	0.0047	0.0115	0.2985	0.0288	0.2254	-25.5939	38.9241	30.4953
8	2.687	-0.1892	-0.1114	1.4063	-0.2765	1.9554	-0.0799	0.2625	0.0525	-0.2324	0.0534	0.084	-0.1348	0.1068	-0.0389	0.1477	-0.0114	-0.0395	0.1228	0.0006	0.1546	-5.3839	46.0114	11.1226
9	1.719	0.2418	-0.1618	1.0545	-0.5806	1.9549	0.1336	0.1129	-0.1788	-0.0683	0.1443	-0.1583	0.5693	0.5592	0.1159	-0.114	-0.0905	0.0443	0.043	-0.0359	0.2141	3.1033	37.9904	20.4443
10	3.192	0.0376	-0.2009	1.5525	-0.4992	2.2494	0.0297	-0.4242	-0.3642	0.0344	-0.0318	-0.0284	0.0501	0.1088	-0.0991	0.1445	-0.045	-0.0368	0.2014	0.028	0.1848	-0.5057	31.8923	35.5359
11	2.1483	-0.2138	0.5744	1.0697	-0.5022	2.1599	0.168	0.2399	-0.4427	-0.3381	0.0639	0.1641	0.4083	-0.4787	-0.1237	0.2392	-0.0792	-0.0228	0.2368	-0.0932	0.1567	-6.2352	36.7408	5.6563
12	5.7703	0.7736	-0.7974	3.4291	1.2106	4.9501	-0.1319	0.3313	-0.2328	0.2464	0.0724	0.3157	0.573	-0.0263	0.0895	0.2363	0.008	-0.083	0.2624	-0.0076	0.1948	-20.3399	41.4907	7.4402
13	1.3917	0.0862	-0.1963	2.2023	-0.3531	1.5646	-0.0557	0.4093	-0.1752	-0.2669	0.1226	0.5504	0.101	-0.4573	-0.0582	0.4965	-0.0301	-0.1941	0.4013	-0.0173	0.3388	3.3134	-10.5368	47.3238
14	1.9733	0.6361	-0.1424	1.7302	-0.12	2.9531	-0.0373	-0.0329	0.0622	0.0259	-0.1397	-0.1085	0.2817	0.2491	0.0576	0.2082	0.0661	-0.094	0.2173	-0.0243	0.206	25.6628	-10.1922	65.5463
15	2.9135	0.0595	-0.1206	2.4782	0.0075	2.8105	-0.1792	-0.101	0.353	-0.4001	0.1026	-0.0663	-0.2993	0.467	0.1065	0.3014	-0.0749	-0.0592	0.2968	0.0515	0.2305	31.9889	3.481	61.6142
16	2.3209	0.5575	-0.4046	1.8402	0.2039	1.5733	-0.0151	0.2083	0.4019	-0.1454	0.0519	0.2336	-0.3862	-0.0048	0.0003	0.501	0.0287	-0.1467	0.3096	0.0669	0.3391	17.5311	10.2119	47.8666
17	1.8531	0.3664	-0.007	3.7389	-0.3206	1.6897	0.1018	0.1494	0.1489	0.3824	-0.0576	0.7091	0.0833	0.0532	-0.1193	0.3116	0.0248	-0.0895	0.1693	0.0004	0.1502	20.0112	-5.438	73.055
18	1.9035	0.9997	0.1917	4.264	0.2046	1.3581	-0.1309	0.396	0.1569	-0.191	-0.1108	0.5865	-0.3274	-0.0173	0.2564	0.2924	-0.0682	-0.0839	0.2907	-0.0036	0.227	11.8585	-19.9979	68.6775
19	0.8381	-0.135	-0.301	1.1378	0.101	0.9876	0.0288	0.4543	-0.2474	-0.8557	0.0313	-1.0305	0.1825	0.2765	-0.0176	1.1018	0.1523	0.4453	0.5892	0.0556	0.6814	2.5322	47.9679	66.5567
20	1.9326	0.0871	-0.3173	1.3214	0.166	0.9149	-0.0481	0.6187	0.0398	-0.9264	-0.0581	-0.1403	-0.0583	-0.3205	0.0154	0.8069	0.0715	0.0384	0.407	0.0047	0.1666	-18.9009	47.4421	74.9392
21	1.7987	-0.548	-1.1129	1.0418	0.4534	1.8315	-0.0116	0.5445	-0.442	-0.4594	-0.1112	-0.2085	0.656	-0.1924	0.3701	0.9045	0.0953	0.1942	0.3877	-0.1527	0.446	-19.5121	28.5579	77.7741
22	1.5537	-0.2226	-0.0914	1.4454	-0.0749	1.3684	0.3787	0.6616	-0.4241	-0.8851	-0.0985	-0.4464	0.3806	-0.2721	-0.1783	1.3493	0.0999	0.2622	0.7605	-0.0907	0.5547	-13.7798	26.2516	65.5266
23	2.8839	0.2796	0.2934	3.4482	0.2968	2.1878	0.0475	0.2881	-0.5058	-0.3159	-0.1049	-0.3916	0.4224	0.0257	0.0296	0.2966	0.0538	0.0712	0.3534	-0.0122	0.1573	-17.9592	36.4792	88.3804
24	2.2959	-1.0442	0.1881	4.6182	-1.0471	1.5683	-0.1066	0.1142	0.0583	0.082	0.0136	-0.2198	0.0587	-0.311	0.0281	0.3031	0.1263	0.0522	0.1518	-0.0301	0.1836	-14.6972	57.1653	90.6732
25	1.5995	-0.1761	-0.7965	3.8979	1.712	2.2058	0.1282	0.1785	0.0766	-0.3371	-0.2515	-1.0401	0.4179	0.3212	0.2253	0.4987	0.0857	0.0454	0.3108	0.1121	0.3223	-6.5244	57.8659	86.5142

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 185 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 186 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 434 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 435 through 477 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 185 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 186 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 194 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 195 through 260 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 261 through 307 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 308 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 484 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 159 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 160 through 273 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 274 through 322 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 323 through 396 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 397 through 421 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 422 through 445 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 446 through 483 )

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