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

ID or keywords:

Entry

Database: PDB / ID: 9ihv

Title

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

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus / complex / maltopentaose / 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 / alpha-maltopentaose / Glycoside hydrolase family 57 N-terminal domain-containing protein

Function and homology information

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.783 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

-
Download

PDBx/mmCIF format	9ihv.cif.gz	416.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9ihv.ent.gz	342.1 KB	Display	PDB format
PDBx/mmJSON format	9ihv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	8zyiC 9ihtC 9ihuC 9ihwC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#24 - Dec 2001 Glycogen Phosphorylase 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

hetero molecules

116 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
58.2 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

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.007, 39.825, 194.286
Angle α, β, γ (deg.)	90.00, 95.82, 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 (strain 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, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose

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: Chemical

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

Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.02 %
Crystal grow	Temperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium citrate, pH 4.2, 20% PEG 3350

-
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: 1.78→193.29 Å / Num. obs: 89674 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.989 / R_merge(I) obs: 0.228 / R_pim(I) all: 0.096 / R_rim(I) all: 0.248 / Χ²: 0.89 / Net I/σ(I): 5.7 / Num. measured all: 596482
Reflection shell	Resolution: 1.78→1.88 Å / % possible obs: 100 % / Redundancy: 6.8 % / R_merge(I) obs: 2.272 / Num. measured all: 87356 / Num. unique obs: 12939 / CC_1/2: 0.419 / R_pim(I) all: 0.939 / R_rim(I) all: 2.462 / Χ²: 0.74 / Net I/σ(I) obs: 1.3

-
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: 1.783→96.643 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2124	4458	4.99 %
R_work	0.1728	-	-
obs	0.1748	89257	99.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.783→96.643 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8088	0	124	572	8784

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8444
X-RAY DIFFRACTION	f_angle_d	0.922	11434
X-RAY DIFFRACTION	f_dihedral_angle_d	6.128	5030
X-RAY DIFFRACTION	f_chiral_restr	0.056	1218
X-RAY DIFFRACTION	f_plane_restr	0.005	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 (%)
1.783-1.8033	0.3519	122	0.3212	2639	X-RAY DIFFRACTION	93
1.8033-1.8245	0.3215	151	0.2927	2713	X-RAY DIFFRACTION	97
1.8245-1.8467	0.3425	138	0.2896	2723	X-RAY DIFFRACTION	98
1.8467-1.8701	0.3153	135	0.2643	2841	X-RAY DIFFRACTION	99
1.8701-1.8947	0.2559	128	0.2512	2833	X-RAY DIFFRACTION	99
1.8947-1.9207	0.2887	152	0.2331	2783	X-RAY DIFFRACTION	100
1.9207-1.9481	0.2285	145	0.2196	2766	X-RAY DIFFRACTION	100
1.9481-1.9772	0.2973	134	0.2178	2919	X-RAY DIFFRACTION	100
1.9772-2.0081	0.2574	172	0.1966	2759	X-RAY DIFFRACTION	100
2.0081-2.041	0.2174	149	0.1843	2791	X-RAY DIFFRACTION	100
2.041-2.0762	0.247	155	0.1842	2829	X-RAY DIFFRACTION	100
2.0762-2.114	0.2245	151	0.1832	2810	X-RAY DIFFRACTION	100
2.114-2.1546	0.2184	136	0.1821	2812	X-RAY DIFFRACTION	100
2.1546-2.1986	0.2251	153	0.1664	2854	X-RAY DIFFRACTION	100
2.1986-2.2464	0.2466	148	0.1641	2819	X-RAY DIFFRACTION	100
2.2464-2.2987	0.2025	138	0.1608	2792	X-RAY DIFFRACTION	100
2.2987-2.3562	0.2032	152	0.1537	2904	X-RAY DIFFRACTION	100
2.3562-2.4199	0.1957	143	0.1573	2786	X-RAY DIFFRACTION	100
2.4199-2.4911	0.1946	147	0.1553	2853	X-RAY DIFFRACTION	100
2.4911-2.5715	0.226	124	0.1563	2837	X-RAY DIFFRACTION	100
2.5715-2.6634	0.2015	184	0.1504	2849	X-RAY DIFFRACTION	100
2.6634-2.7701	0.1784	152	0.1506	2810	X-RAY DIFFRACTION	100
2.7701-2.8962	0.1782	153	0.1447	2833	X-RAY DIFFRACTION	100
2.8962-3.0489	0.1771	145	0.1471	2925	X-RAY DIFFRACTION	100
3.0489-3.2399	0.1819	129	0.1556	2808	X-RAY DIFFRACTION	100
3.2399-3.4901	0.1882	146	0.1499	2860	X-RAY DIFFRACTION	100
3.4901-3.8413	0.1827	173	0.1425	2867	X-RAY DIFFRACTION	100
3.8413-4.3971	0.1821	163	0.1415	2889	X-RAY DIFFRACTION	100
4.3971-5.5399	0.1855	159	0.151	2913	X-RAY DIFFRACTION	100
5.5399-96.643	0.2214	181	0.1956	2982	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	0.7403	0.1522	-0.0319	0.5043	-0.1167	0.4331	-0.0425	-0.0698	-0.1282	-0.0662	0.0333	0.0251	0.1136	-0.0254	0.0143	0.043	-0.0155	-0.0051	0.0428	0.0111	0.0703	-9.9235	11.1082	70.049
2	0.8656	-0.3373	-0.4928	0.2796	0.1997	1.0853	-0.057	-0.3142	0.0683	0.0622	0.0505	0.0058	0.0671	-0.0102	-0.024	0.1022	-0.0065	-0.0175	0.2452	-0.0053	0.1094	-19.4329	17.6568	89.4498
3	1.1683	0.0618	-0.7677	0.512	-0.0867	1.1455	0.0608	0.0623	0.1893	-0.0182	-0.0326	0.0295	-0.1528	-0.3212	0.0029	0.0113	-0.0233	-0.0107	0.1248	0.0101	0.1116	-25.1912	19.2286	76.8609
4	0.8705	-0.1429	0.148	0.2711	-0.0781	0.9537	-0.0189	0.07	-0.0725	-0.0831	0.0456	-0.0234	0.0212	0.1863	-0.0105	0.0429	-0.0229	0.0032	0.0416	-0.0054	0.0855	7.5552	12.0485	65.3375
5	1.0408	0.1155	-0.139	0.5286	-0.0721	1.3678	0.0233	0.1197	0.0025	-0.2528	0.0689	0.0732	-0.1893	0.0064	-0.0666	0.1344	-0.0386	-0.0272	0.0533	0.0308	0.072	-7.7446	19.7386	52.624
6	0.855	0.237	0.2008	0.7351	0.1191	1.3876	-0.0722	-0.1114	0.1528	0.0502	0.0205	-0.1381	-0.2567	0.2551	0.0293	-0.0109	-0.0149	-0.009	0.1319	-0.0103	0.0887	12.4341	18.0014	75.8815
7	2.6399	-0.0305	0.2033	0.7701	0.1597	1.7746	-0.0142	-0.3356	0.0874	0.2709	-0.0921	0.0238	-0.1377	-0.0427	-0.0105	-0.0243	-0.0095	-0.0281	0.1928	0.0041	0.0618	2.2026	14.1749	86.4348
8	1.1334	0.1558	-0.2727	0.3924	-0.0579	0.7806	-0.048	0.2512	-0.1064	-0.0481	-0.0248	-0.0165	0.0723	0.0063	0.0346	0.0937	0.0218	-0.0129	0.0934	-0.0162	0.0665	-23.6436	31.8273	19.6454
9	1.0721	-0.2043	-0.2551	0.5217	0.1046	1.7008	0.0251	0.2454	0.0208	-0.0479	-0.0344	-0.0209	-0.1003	0.471	0.0294	0.0731	0.0197	0.0106	0.1593	0.0026	0.0908	-11.3099	37.2623	16.5965
10	1.0238	0.0997	-0.1902	0.6078	0.0597	1.0827	0.0256	0.1114	-0.1702	0.0247	0.0207	0.0333	0.1612	-0.2074	-0.009	0.1053	-0.01	-0.0126	0.0541	-0.0141	0.1015	-43.8801	27.0273	30.0623
11	0.5995	-0.0835	0.1915	0.6172	-0.1031	0.8145	0.1905	0.0812	0.2168	0.2265	-0.0282	0.0668	-0.365	-0.2631	0.0544	0.1995	0.0016	0.045	-0.0186	-0.045	0.0831	-32.9803	41.4797	42.0651
12	1.1417	0.1813	-0.0018	0.5557	0.0282	0.7223	0.0609	0.003	0.057	0.0737	-0.0398	0.0207	-0.0666	-0.0668	-0.0237	0.0999	0.0057	0.0151	0.0309	-0.0068	0.0727	-36.2522	36.1465	34.2295
13	2.3908	-0.0123	-0.0115	1.3502	-0.1939	2.4469	-0.0061	0.4124	0.077	-0.1084	-0.0295	-0.0598	-0.0233	-0.1036	0.0083	0.0936	0.0086	-0.0166	0.2096	-0.0028	0.0656	-40.5199	32.7538	12.1618

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 185 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 186 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 185 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 186 through 278 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 279 through 360 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 361 through 435 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 436 through 477 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi