PDB-9k7d: Crystal structure of GH57 family amylopullulanase from Aquifex ae...

ID or keywords:

Entry

Database: PDB / ID: 9k7d

Title

Crystal structure of GH57 family amylopullulanase from Aquifex aeolicus mutant E256Q in complex with Maltohexaose

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 / 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: 1.72 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: 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	Oct 23, 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	9k7d.cif.gz	421.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9k7d.ent.gz	348.6 KB	Display	PDB format
PDBx/mmJSON format	9k7d.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/k7/9k7d ftp://data.pdbj.org/pub/pdb/validation_reports/k7/9k7d	HTTPS FTP

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Related structure data

Related structure data	8zyiC 9ihtC 9ihuC 9ihvC 9ihwC 9ihxC 9ii0C 9ii1C 9k7cC 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

118 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
59.1 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
59.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.420, 40.790, 196.760
Angle α, β, γ (deg.)	90.00, 95.99, 90.00
Int Tables number	3
Space group name H-M	P121

#1: Protein

Glycoside hydrolase family 57 N-terminal domain-containing protein

Mass: 57252.250 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-(1-4)-alpha-D- ...

Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}	LINUCS	PDB-CARE

#3: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...

Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}	LINUCS	PDB-CARE

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.08 Å³/Da / Density % sol: 40.75 %
Crystal grow	Temperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1M 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 EIGER X 9M / Detector: PIXEL / Date: Oct 17, 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: 1.72→39.14 Å / Num. obs: 104038 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.993 / R_merge(I) obs: 0.2 / R_pim(I) all: 0.085 / R_rim(I) all: 0.217 / Χ²: 0.94 / Net I/σ(I): 10.1 / Num. measured all: 696967
Reflection shell	Resolution: 1.72→1.76 Å / % possible obs: 100 % / Redundancy: 6.9 % / R_merge(I) obs: 1.348 / Num. measured all: 52608 / Num. unique obs: 7655 / CC_1/2: 0.567 / R_pim(I) all: 0.549 / R_rim(I) all: 1.457 / Χ²: 0.91 / Net I/σ(I) obs: 1.5

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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: 1.72→39.137 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2127	5147	4.95 %
R_work	0.1726	-	-
obs	0.1746	104016	99.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.72→39.137 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8334	0	0	587	8921

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8596
X-RAY DIFFRACTION	f_angle_d	1.018	11664
X-RAY DIFFRACTION	f_dihedral_angle_d	4.141	7188
X-RAY DIFFRACTION	f_chiral_restr	0.076	1280
X-RAY DIFFRACTION	f_plane_restr	0.006	1428

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 (%)
1.72-1.7396	0.3045	175	0.2531	3231	X-RAY DIFFRACTION	100
1.7396-1.76	0.3127	150	0.26	3380	X-RAY DIFFRACTION	100
1.76-1.7815	0.3186	163	0.2488	3213	X-RAY DIFFRACTION	100
1.7815-1.804	0.2992	163	0.2713	3285	X-RAY DIFFRACTION	100
1.804-1.8278	0.327	176	0.2577	3239	X-RAY DIFFRACTION	100
1.8278-1.8528	0.2897	196	0.2345	3327	X-RAY DIFFRACTION	100
1.8528-1.8793	0.2626	180	0.2225	3173	X-RAY DIFFRACTION	100
1.8793-1.9073	0.2493	161	0.197	3250	X-RAY DIFFRACTION	100
1.9073-1.9371	0.2477	185	0.2071	3343	X-RAY DIFFRACTION	100
1.9371-1.9689	0.2621	165	0.1984	3230	X-RAY DIFFRACTION	100
1.9689-2.0029	0.2438	177	0.2008	3266	X-RAY DIFFRACTION	100
2.0029-2.0393	0.2464	187	0.1907	3303	X-RAY DIFFRACTION	100
2.0393-2.0785	0.2524	166	0.1886	3210	X-RAY DIFFRACTION	100
2.0785-2.1209	0.2646	177	0.1896	3329	X-RAY DIFFRACTION	100
2.1209-2.167	0.2209	203	0.1806	3265	X-RAY DIFFRACTION	100
2.167-2.2174	0.2141	161	0.1855	3230	X-RAY DIFFRACTION	100
2.2174-2.2729	0.2066	188	0.1733	3334	X-RAY DIFFRACTION	100
2.2729-2.3343	0.1988	158	0.1682	3189	X-RAY DIFFRACTION	100
2.3343-2.403	0.2253	174	0.1752	3348	X-RAY DIFFRACTION	100
2.403-2.4806	0.2322	160	0.1815	3299	X-RAY DIFFRACTION	100
2.4806-2.5692	0.2226	170	0.1763	3294	X-RAY DIFFRACTION	100
2.5692-2.672	0.21	163	0.1689	3302	X-RAY DIFFRACTION	100
2.672-2.7936	0.2031	166	0.1665	3306	X-RAY DIFFRACTION	100
2.7936-2.9409	0.1927	151	0.1691	3369	X-RAY DIFFRACTION	100
2.9409-3.125	0.2198	162	0.1626	3298	X-RAY DIFFRACTION	100
3.125-3.3662	0.1802	183	0.1568	3305	X-RAY DIFFRACTION	100
3.3662-3.7047	0.176	178	0.1435	3346	X-RAY DIFFRACTION	100
3.7047-4.2403	0.1546	155	0.1356	3327	X-RAY DIFFRACTION	100
4.2403-5.3401	0.1643	170	0.135	3384	X-RAY DIFFRACTION	100
5.3401-39.137	0.2123	184	0.1755	3494	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	2.0694	0.0887	0.1276	1.5252	0.2026	3.0262	0.0574	0.3323	0.1882	-0.1999	-0.0906	0.1817	-0.2108	-0.3082	-0.0173	0.1418	0.0201	-0.0083	0.2069	0.0297	0.2154	-49.0356	42.3574	24.1526
2	3.5867	0.3781	-0.0233	2.1697	0.0863	3.2356	-0.0081	0.5056	0.0362	-0.2696	0.0061	0.0497	-0.1222	-0.0498	-0.0014	0.1841	0.0211	-0.0436	0.2703	-0.0072	0.1231	-40.6052	36.6194	12.6566
3	1.146	-0.0352	-0.3151	0.345	0.0839	0.7588	-0.0142	-0.0797	-0.087	0.0321	0.0051	0.0301	0.0531	-0.0902	0.0095	0.1028	-0.0279	0.0042	0.103	-0.0011	0.1204	-12.7166	15.6964	74.3637
4	2.3981	0.439	-0.7358	1.1972	-0.4387	3.4438	0.0996	-0.3219	0.3521	0.137	-0.028	0.0491	-0.4855	-0.0416	-0.0382	0.2075	-0.0201	0.0382	0.1779	-0.0411	0.2065	-21.851	31.223	87.6711
5	1.5878	-0.2872	-1.0905	0.6718	0.6429	2.1245	0.0322	0.0921	-0.0157	0.0142	-0.0631	0.1023	0.0418	-0.3324	0.0678	0.0903	-0.03	-0.0002	0.1498	0.0028	0.1627	-26.0974	18.7083	75.7439
6	1.4606	0.1466	0.3894	0.5395	0.0566	1.1119	0.0245	-0.0058	-0.0803	-0.0085	-0.0438	-0.0405	0.0776	0.132	0.0178	0.1142	-0.0008	0.0155	0.0971	-0.007	0.135	8.2175	13.0444	69.2389
7	1.4454	-0.9843	-0.2845	1.4482	-0.0581	1.056	0.0189	0.1442	0.2393	0.0472	-0.0458	-0.1971	-0.0946	0.1625	0.016	0.1465	-0.0424	0.0073	0.1606	0.0117	0.2014	5.1092	27.6699	58.5226
8	2.1705	0.061	-0.7226	1.093	-0.2322	2.7322	0.0635	0.33	0.1269	-0.1809	0.0367	0.0036	-0.153	-0.1538	-0.0871	0.1449	-0.0198	-0.001	0.1302	0.0174	0.1398	-8.2033	27.7304	54.5527
9	1.3534	-0.0485	0.1404	0.8384	0.0735	2.3494	-0.0139	-0.1502	0.137	0.0876	-0.0472	-0.0486	-0.2272	0.1104	0.0607	0.1133	-0.0338	-0.0025	0.1546	-0.008	0.1918	12.0815	21.7823	77.2673
10	3.5488	-0.8873	-0.1224	3.0685	-0.4871	2.5789	-0.0677	-0.274	0.0211	0.1354	0.0573	-0.0266	-0.0975	-0.0096	0.0241	0.1076	-0.0229	-0.0039	0.1857	0.0051	0.1142	1.8375	16.2577	87.0416
11	1.6016	0.0961	0.1287	0.7036	0.0306	0.9293	0.0611	0.0917	-0.0926	-0.0172	-0.0177	-0.0303	0.1626	0.0172	-0.0204	0.1583	0.0034	-0.0039	0.0976	0.0063	0.1322	-25.9699	35.8035	27.2354
12	0.9031	0.5038	-0.3683	0.3229	0.0157	2.0917	0.0175	0.3635	-0.1133	-0.1844	0.0351	-0.0352	0.0847	0.1875	-0.0023	0.2484	-0.0131	-0.0184	0.3662	-0.0151	0.2024	-19.6696	39.2477	5.7809
13	1.5765	0.1306	-0.5775	0.6885	-0.189	2.2687	0.0224	0.1721	0.0342	-0.0838	0.0084	-0.1291	-0.0608	0.4241	-0.0133	0.1588	-0.0092	-0.0078	0.2394	-0.0268	0.1792	-12.9304	41.2197	18.3412
14	1.6998	-0.4276	-0.2702	1.275	0.1558	1.3975	0.062	0.0598	-0.144	-0.0089	-0.0706	0.166	0.1572	-0.2823	-0.0101	0.1369	-0.0511	-0.0096	0.1328	-0.0016	0.1449	-45.4482	33.3987	30.7175
15	2.3681	1.1387	-0.5894	1.4117	-0.099	1.3618	0.0337	-0.2534	0.2127	0.0479	-0.0894	0.1243	-0.0966	-0.0569	0.0242	0.1437	0.0001	-0.0102	0.1204	-0.0126	0.1587	-38.7758	47.8743	41.2081
16	1.9049	-0.0151	-0.4696	1.1735	-0.3578	2.6564	0.0149	-0.2238	0.1915	0.1291	0.0086	-0.0568	-0.1952	-0.027	-0.0699	0.1889	0.0077	-0.0102	0.1398	-0.0179	0.1753	-27.1093	51.0859	41.5734
17	1.9812	-0.529	0.1085	1.2598	0.5598	2.5491	0.0561	-0.3579	-0.0139	0.3171	-0.0026	-0.0533	0.0537	0.1086	-0.0395	0.1756	-0.005	-0.0364	0.1381	-0.0042	0.1555	-23.2197	43.2327	44.939

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 397 through 435 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 436 through 477 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 2 through 88 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 123 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 124 through 185 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 186 through 278 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 279 through 322 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 323 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 68 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 69 through 102 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 103 through 194 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 195 through 278 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 279 through 322 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 323 through 360 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 361 through 396 )

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