PDB-9ii0: Crystal structure of GH57 family amylopullulanase mutant D352N fr...

ID or keywords:

Entry

Database: PDB / ID: 9ii0

Title

Crystal structure of GH57 family amylopullulanase mutant D352N from Aquifex aeolicus in complex with Maltooctaose

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus / complex / mutant

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: 1.89 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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PDBx/mmCIF format	9ii0.cif.gz	416.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9ii0.ent.gz	343.7 KB	Display	PDB format
PDBx/mmJSON format	9ii0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ii0_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9ii0_full_validation.pdf.gz	1 MB	Display
Data in XML	9ii0_validation.xml.gz	44.4 KB	Display
Data in CIF	9ii0_validation.cif.gz	59.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ii/9ii0 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/9ii0	HTTPS FTP

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Related structure data

Related structure data	8zyiC 9ihtC 9ihuC 9ihvC 9ihwC 9ihxC 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

117 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&software
Evidence: gel filtration
58.5 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&software
58.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.070, 40.350, 195.390
Angle α, β, γ (deg.)	90.00, 96.01, 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: D352N
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: 1153.001 Da / Num. of mol.: 2 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1	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]{[(4+1)][a-D-Glcp]{}}}}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.14 Å³/Da / Density % sol: 42.42 %
Crystal grow	Temperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium citrate, pH 4.2, 20% PEG 3350 / Temp details: 368

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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: Nov 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.74→61.041 Å / Num. obs: 98778 / % possible obs: 98.4 % / Redundancy: 6.7 % / CC_1/2: 0.995 / R_merge(I) obs: 0.16 / R_pim(I) all: 0.068 / R_rim(I) all: 0.174 / Χ²: 1.04 / Net I/σ(I): 7.9
Reflection shell	Resolution: 1.74→1.79 Å / % possible obs: 97.1 % / Redundancy: 6.7 % / R_merge(I) obs: 1.893 / Num. measured all: 47977 / Num. unique obs: 7145 / CC_1/2: 0.459 / R_pim(I) all: 0.786 / R_rim(I) all: 2.052 / Χ²: 0.99 / Net I/σ(I) obs: 1.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.89→42.157 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2077	3832	4.99 %
R_work	0.1677	-	-
obs	0.1697	76749	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.89→42.157 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8250	0	0	315	8565

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8488
X-RAY DIFFRACTION	f_angle_d	1.046	11501
X-RAY DIFFRACTION	f_dihedral_angle_d	5.689	5056
X-RAY DIFFRACTION	f_chiral_restr	0.059	1238
X-RAY DIFFRACTION	f_plane_restr	0.007	1424

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 (%)
1.89-1.9139	0.3437	138	0.2805	2753	X-RAY DIFFRACTION	100
1.9139-1.9391	0.3443	139	0.2608	2612	X-RAY DIFFRACTION	100
1.9391-1.9657	0.2822	156	0.2483	2664	X-RAY DIFFRACTION	100
1.9657-1.9938	0.2887	127	0.2291	2678	X-RAY DIFFRACTION	100
1.9938-2.0235	0.2643	129	0.2207	2733	X-RAY DIFFRACTION	100
2.0235-2.0551	0.28	130	0.2157	2636	X-RAY DIFFRACTION	100
2.0551-2.0888	0.2258	111	0.1997	2733	X-RAY DIFFRACTION	100
2.0888-2.1248	0.2561	135	0.1867	2702	X-RAY DIFFRACTION	100
2.1248-2.1635	0.2545	149	0.1961	2641	X-RAY DIFFRACTION	100
2.1635-2.2051	0.2295	157	0.1903	2680	X-RAY DIFFRACTION	100
2.2051-2.2501	0.2279	129	0.186	2749	X-RAY DIFFRACTION	100
2.2501-2.299	0.2237	111	0.1823	2669	X-RAY DIFFRACTION	100
2.299-2.3525	0.2121	138	0.1834	2731	X-RAY DIFFRACTION	100
2.3525-2.4113	0.2165	130	0.1768	2661	X-RAY DIFFRACTION	100
2.4113-2.4765	0.2205	138	0.1722	2684	X-RAY DIFFRACTION	100
2.4765-2.5494	0.2146	155	0.1679	2698	X-RAY DIFFRACTION	100
2.5494-2.6316	0.2309	129	0.1631	2683	X-RAY DIFFRACTION	100
2.6316-2.7257	0.2077	149	0.1629	2717	X-RAY DIFFRACTION	100
2.7257-2.8348	0.1946	167	0.1551	2656	X-RAY DIFFRACTION	100
2.8348-2.9638	0.1919	156	0.1602	2698	X-RAY DIFFRACTION	100
2.9638-3.12	0.2188	154	0.1614	2687	X-RAY DIFFRACTION	99
3.12-3.3154	0.2113	168	0.153	2693	X-RAY DIFFRACTION	100
3.3154-3.5713	0.1691	170	0.1531	2699	X-RAY DIFFRACTION	100
3.5713-3.9304	0.1745	118	0.143	2732	X-RAY DIFFRACTION	100
3.9304-4.4986	0.1888	136	0.1398	2752	X-RAY DIFFRACTION	99
4.4986-5.6656	0.1759	158	0.15	2753	X-RAY DIFFRACTION	99
5.6656-42.157	0.1996	155	0.1695	2823	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	1.6226	-0.5077	0.0276	0.4766	-0.195	0.9258	0.0903	-0.1856	-0.2004	-0.0373	-0.019	0.0698	0.2392	-0.1051	-0.0146	0.2131	-0.0273	-0.0116	0.1604	0.0152	0.2091	14.8088	-24.16	72.7772
2	1.2315	0.1973	-0.3516	0.8783	-0.2302	2.1699	0.1486	-0.5228	0.2029	0.1422	0.046	0.0294	-0.1321	-0.1746	-0.0493	0.2502	-0.0089	0.023	0.4041	-0.0301	0.2686	5.9969	-9.8987	89.8936
3	1.531	-0.2176	-0.3277	0.7443	0.3873	1.6953	0.0772	-0.275	-0.1987	-0.0412	-0.0417	0.1563	0.2298	-0.4164	0.009	0.2191	-0.0513	-0.0169	0.3124	0.0598	0.2742	0.7058	-21.0532	78.3092
4	1.6373	-0.55	0.0345	0.9109	0.2167	1.4509	0.0788	-0.1274	-0.2165	-0.0056	0.0297	-0.0998	0.2779	0.3498	-0.0525	0.2676	0.0718	-0.0246	0.2583	0.0125	0.2393	34.5056	-26.5785	69.6046
5	1.7048	-0.5547	0.1649	0.7893	-0.2545	1.5949	0.1225	0.163	0.0686	-0.1693	-0.1046	-0.0687	0.0947	0.2517	-0.0268	0.2307	0.0396	0.0296	0.1554	0.0117	0.2125	30.3615	-18.7508	57.6491
6	1.5599	-0.1766	-0.2596	1.202	0.1852	1.9506	0.2136	0.2288	0.3046	-0.2864	-0.1496	-0.0449	-0.1564	0.0297	-0.0446	0.2874	0.0708	0.032	0.1725	0.0608	0.2121	17.2712	-9.3231	55.0888
7	1.9388	0.0883	-0.6392	0.7551	0.0623	2.103	0.0962	0.4647	-0.0963	-0.1851	-0.1129	0.1811	0.1235	-0.1569	-0.0401	0.2528	0.0658	-0.0405	0.2376	0.0121	0.2161	13.3652	-17.1336	52.0362
8	1.0625	0.0241	0.1544	0.901	0.1378	1.7942	0.027	-0.1971	0.2877	0.0235	-0.1395	-0.2044	-0.075	0.5026	0.0201	0.2011	0.0133	0.0085	0.3254	-0.0249	0.2797	38.7461	-17.3997	73.0296
9	2.7104	-0.2563	-0.1008	1.6062	-0.0828	2.4925	0.0118	-0.4251	0.0905	0.1614	0.112	-0.037	0.1204	-0.0089	-0.017	0.2222	0.0032	-0.0345	0.2882	0.0079	0.1853	30.2938	-22.5179	84.6841
10	1.0006	-0.1032	0.1925	0.3536	-0.0459	0.3503	-0.1051	0.0652	-0.0829	0.0466	0.0555	-0.0246	0.0684	0.0715	0.0086	0.1965	0.0453	-0.0011	0.2011	-0.0244	0.1892	2.5064	-41.8588	22.5849
11	1.2903	0.1557	-0.8655	0.6004	-0.0404	1.5039	-0.0047	0.0574	0.1416	-0.0396	0.0058	-0.1111	-0.1017	0.193	0.0236	0.1921	0.0223	-0.0171	0.2655	-0.0016	0.2469	14.2714	-33.3786	17.9957
12	1.0074	-0.0634	0.2574	0.4233	0.0009	1.1692	-0.135	-0.1297	-0.0612	0.1196	0.1107	0.1075	0.0258	-0.2025	0.0169	0.2343	0.084	0.0289	0.224	0.009	0.2046	-17.3577	-41.0737	31.4183
13	1.177	-0.2965	-0.2038	0.8053	0.2613	1.5912	-0.1456	-0.2866	0.0212	0.2442	0.1196	-0.0563	-0.204	-0.0404	-0.0463	0.3421	0.1448	-0.0584	0.2873	-0.0413	0.209	-2.1422	-33.2299	44.0537
14	1.0934	-0.1026	0.1754	0.8614	-0.0341	1.7756	-0.1645	0.0362	0.0979	0.0383	0.0224	0.0875	-0.2263	-0.2356	0.0108	0.1923	0.0557	0.0088	0.2962	-0.0126	0.22	-22.272	-35.397	20.7281
15	2.8155	0.2725	-0.0358	0.9982	-0.1897	2.3165	-0.1182	0.3215	0.069	-0.0205	0.0325	-0.0259	-0.1024	0.0528	0.0398	0.1655	0.0129	-0.005	0.2744	0.0014	0.1889	-12.0443	-39.2588	10.1946

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 123 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 124 through 185 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 186 through 245 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 246 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 2 through 88 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 89 through 185 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 186 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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