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

ID or keywords:

Entry

Database: PDB / ID: 9ihw

Title

Crystal structure of GH57 family amylopullulanase mutant D352N from Aquifex aeolicusin complex with Maltohexaose

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: 1.64 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	9ihw.cif.gz	420.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9ihw.ent.gz	345.9 KB	Display	PDB format
PDBx/mmJSON format	9ihw.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/ih/9ihw ftp://data.pdbj.org/pub/pdb/validation_reports/ih/9ihw	HTTPS FTP

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Related structure data

Related structure data	8zyiC 9ihtC 9ihuC 9ihvC 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

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
Evidence: gel filtration
58.6 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
58.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.330, 41.150, 194.150
Angle α, β, γ (deg.)	90.00, 96.15, 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: 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

#3: Chemical

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

Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.13 Å³/Da / Density % sol: 42.18 %
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: Oct 5, 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: 1.64→64.34 Å / Num. obs: 118846 / % possible obs: 99.9 % / Redundancy: 6 % / CC_1/2: 0.99 / R_merge(I) obs: 0.199 / R_pim(I) all: 0.091 / R_rim(I) all: 0.22 / Χ²: 0.9 / Net I/σ(I): 9.9 / Num. measured all: 712495
Reflection shell	Resolution: 1.64→1.68 Å / % possible obs: 99.9 % / Redundancy: 5.2 % / R_merge(I) obs: 1.417 / Num. measured all: 45146 / Num. unique obs: 8687 / CC_1/2: 0.513 / R_pim(I) all: 0.695 / R_rim(I) all: 1.584 / Χ²: 0.83 / 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: 1.64→60.977 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.71 / Phase error: 19.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1998	5863	4.93 %
R_work	0.1685	-	-
obs	0.17	118828	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: 1.64→60.977 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8224	0	6	617	8847

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8473
X-RAY DIFFRACTION	f_angle_d	0.883	11479
X-RAY DIFFRACTION	f_dihedral_angle_d	5.037	7080
X-RAY DIFFRACTION	f_chiral_restr	0.051	1230
X-RAY DIFFRACTION	f_plane_restr	0.006	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 (%)
1.64-1.6586	0.2924	203	0.2744	3701	X-RAY DIFFRACTION	100
1.6586-1.6782	0.307	169	0.2675	3728	X-RAY DIFFRACTION	100
1.6782-1.6986	0.2667	199	0.2553	3741	X-RAY DIFFRACTION	100
1.6986-1.7201	0.2436	179	0.2416	3793	X-RAY DIFFRACTION	100
1.7201-1.7428	0.2692	197	0.2242	3681	X-RAY DIFFRACTION	100
1.7428-1.7666	0.2441	188	0.2199	3774	X-RAY DIFFRACTION	100
1.7666-1.7919	0.234	191	0.2096	3783	X-RAY DIFFRACTION	100
1.7919-1.8186	0.2528	192	0.1991	3671	X-RAY DIFFRACTION	100
1.8186-1.847	0.2737	179	0.1963	3806	X-RAY DIFFRACTION	100
1.847-1.8773	0.2192	209	0.1882	3719	X-RAY DIFFRACTION	100
1.8773-1.9097	0.2504	170	0.1869	3749	X-RAY DIFFRACTION	100
1.9097-1.9444	0.2097	205	0.1732	3781	X-RAY DIFFRACTION	100
1.9444-1.9818	0.2148	214	0.1738	3715	X-RAY DIFFRACTION	100
1.9818-2.0223	0.1998	205	0.1689	3710	X-RAY DIFFRACTION	100
2.0223-2.0663	0.2278	185	0.1684	3806	X-RAY DIFFRACTION	100
2.0663-2.1143	0.1877	175	0.1667	3764	X-RAY DIFFRACTION	100
2.1143-2.1672	0.2198	192	0.1685	3781	X-RAY DIFFRACTION	100
2.1672-2.2258	0.1992	210	0.1705	3704	X-RAY DIFFRACTION	100
2.2258-2.2913	0.1983	215	0.1691	3776	X-RAY DIFFRACTION	100
2.2913-2.3653	0.2247	208	0.1748	3711	X-RAY DIFFRACTION	100
2.3653-2.4498	0.2285	169	0.1747	3837	X-RAY DIFFRACTION	100
2.4498-2.5479	0.2005	196	0.1674	3775	X-RAY DIFFRACTION	100
2.5479-2.6639	0.1925	154	0.1618	3754	X-RAY DIFFRACTION	100
2.6639-2.8043	0.1837	191	0.1585	3803	X-RAY DIFFRACTION	100
2.8043-2.98	0.1864	200	0.1574	3778	X-RAY DIFFRACTION	100
2.98-3.2101	0.1731	235	0.1511	3793	X-RAY DIFFRACTION	100
3.2101-3.5331	0.198	176	0.144	3803	X-RAY DIFFRACTION	100
3.5331-4.0442	0.1534	203	0.1303	3830	X-RAY DIFFRACTION	100
4.0442-5.0949	0.1576	221	0.1404	3850	X-RAY DIFFRACTION	100
5.0949-60.977	0.2043	233	0.1823	3848	X-RAY DIFFRACTION	97

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	0.8656	-0.0832	-0.3621	0.3033	0.1247	1.0912	-0.0304	-0.076	-0.051	0.0081	0.0311	0.0248	0.0567	-0.0316	0.0074	0.0807	-0.0164	0.0066	0.0907	0.0065	0.1203	-13.5847	16.7035	76.1473
2	1.9446	-0.5027	-1.3427	0.884	0.4019	1.9593	0.054	0.0264	0.1521	0.0173	-0.0057	0.1043	-0.123	-0.1918	0.0098	0.0711	-0.0052	-0.006	0.1222	0.0138	0.1427	-25.8762	22.6867	76.7464
3	2.9673	1.2022	1.2631	0.845	0.855	1.6069	-0.0061	-0.0325	-0.0521	-0.0096	-0.0038	-0.0506	0.0739	0.1043	-0.0093	0.087	0.0109	0.0244	0.0654	-0.0027	0.1262	8.0987	11.6954	72.8503
4	1.3161	-0.4094	-0.0993	0.3571	-0.0951	0.7308	-0.0013	0.1157	-0.0221	-0.0628	-0.0153	-0.0655	0.0445	0.1146	0.0164	0.1021	-0.0265	0.0178	0.1006	-0.0203	0.1164	6.1348	17.925	59.5497
5	1.9736	-0.1669	-0.9591	1.1761	0.2627	2.6325	0.0362	0.2842	0.0187	-0.1822	0.0233	0.0261	-0.0919	-0.0362	-0.0553	0.1048	-0.0307	-0.0083	0.1014	0.0053	0.097	-7.9969	23.4941	52.6235
6	0.8387	-0.0146	0.2057	0.684	0.0727	4.0067	-0.0362	-0.0973	0.1012	0.0113	0.0163	-0.0248	-0.2526	0.1353	0.0187	0.047	-0.0204	0.0099	0.1189	-0.0153	0.1637	11.9324	21.0524	75.8344
7	5.4367	-0.9285	-0.0608	3.6718	0.0251	4.8839	-0.0577	-0.3721	0.0489	0.0833	0.0156	0.0921	-0.1199	-0.0955	0.0132	0.0359	-0.0178	0.0005	0.1441	-0.0134	0.0858	1.7025	16.9758	86.4325
8	1.0552	0.2254	-0.5964	0.4908	-0.1833	1.5798	-0.0409	0.1791	-0.0549	-0.0984	0.0121	-0.0095	0.1707	0.1596	0.0127	0.1533	0.0366	-0.0133	0.1512	-0.0206	0.1145	-24.0718	36.5431	19.7359
9	3.5319	0.6152	-2.3438	1.9575	-1.0796	4.871	0.3646	0.2273	0.6392	0.0605	-0.1935	-0.0659	-0.622	0.2939	-0.2526	0.2552	-0.023	0.0257	0.2795	0.0549	0.2589	-13.8124	54.2646	12.3946
10	1.8448	0.5651	-1.3204	1.0982	-0.9125	3.1985	-0.02	0.0252	-0.0284	-0.0666	-0.0231	-0.0807	0.2245	0.5691	0.1497	0.1592	0.0685	-0.014	0.2839	-0.028	0.151	-11.1507	37.8814	18.7452
11	2.4615	-0.477	0.1233	1.3628	-0.3743	2.1211	0.0512	0.1247	-0.1914	-0.1323	0.0627	0.233	0.2945	-0.3164	-0.0804	0.2035	-0.0281	-0.0229	0.1421	-0.0048	0.1635	-44.9712	31.5936	26.639
12	2.712	-0.2808	-0.5102	2.5861	0.0306	2.6828	-0.0184	-0.1112	-0.2507	0.1095	0.0558	0.0542	0.402	-0.1105	-0.0557	0.1601	-0.0188	-0.0106	0.1003	0.0046	0.131	-42.7351	30.2734	35.7476
13	2.0412	0.8527	-0.6792	1.1386	-0.529	2.1241	0.0948	-0.1411	0.2064	0.0343	-0.0452	0.1668	-0.196	-0.1315	-0.0975	0.1554	0.0364	0.0048	0.114	-0.0204	0.1577	-39.5078	44.1375	41.689
14	1.7357	0.1974	-0.7029	0.9444	-0.4209	2.7283	0.0741	-0.2147	0.1691	0.1644	-0.0813	0.0391	-0.357	0.1669	-0.0401	0.178	-0.0059	-0.002	0.0976	-0.0325	0.1255	-27.9846	47.861	42.4534
15	2.1531	0.1902	-0.6376	0.7443	-0.2875	3.1343	0.1084	-0.235	-0.0122	0.1869	-0.0716	-0.0258	-0.1138	0.3078	0.0168	0.1612	0.007	-0.0244	0.1369	-0.023	0.1346	-23.9708	40.0003	44.9779
16	1.2927	0.055	0.5651	1.021	-0.5277	6.3291	-0.0128	0.3008	0.1466	-0.1118	0.1085	0.144	-0.077	-0.4444	-0.0261	0.098	0.0062	-0.0171	0.1947	0.0365	0.1971	-49.2788	40.9991	24.0299
17	6.0406	0.9329	0.6285	4.0208	0.1193	5.3661	-0.0664	0.6052	0.0728	-0.3352	0.1127	0.0131	0.151	-0.0422	-0.0227	0.1626	0.0083	-0.0398	0.2444	0.006	0.0932	-40.808	36.5146	11.9712

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 102 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 103 through 185 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 186 through 245 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 246 through 322 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 323 through 396 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 397 through 435 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 436 through 477 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 102 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 103 through 123 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 124 through 185 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 186 through 245 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 246 through 278 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 279 through 322 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 323 through 360 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 361 through 396 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 397 through 435 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 436 through 477 )

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