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

ID or keywords:

Entry

Database: PDB / ID: 9jlw

Title

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

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: 1.95 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: 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	9jlw.cif.gz	410.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9jlw.ent.gz	338.2 KB	Display	PDB format
PDBx/mmJSON format	9jlw.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/jl/9jlw ftp://data.pdbj.org/pub/pdb/validation_reports/jl/9jlw	HTTPS FTP

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Related structure data

Related structure data	9jlqC 9jlrC 9jlsC 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
58.5 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
58.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.420, 41.150, 193.210
Angle α, β, γ (deg.)	90.00, 94.48, 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/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.: 1 / 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: 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.: 1 / 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: Chemical

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

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

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 345 / 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: 42.14 %
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 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: 1.95→64.21 Å / Num. obs: 70504 / % possible obs: 99.4 % / Redundancy: 6.5 % / CC_1/2: 0.993 / R_rim(I) all: 0.223 / Net I/σ(I): 6.6
Reflection shell	Resolution: 1.95→2 Å / R_merge(I) obs: 1.398 / Num. unique obs: 5134 / CC_1/2: 0.459 / R_rim(I) all: 1.653

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→59.718 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2328	3508	4.98 %
R_work	0.1949	-	-
obs	0.1968	70478	99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→59.718 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8245	0	0	345	8590

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8480
X-RAY DIFFRACTION	f_angle_d	0.81	11488
X-RAY DIFFRACTION	f_dihedral_angle_d	4.833	5051
X-RAY DIFFRACTION	f_chiral_restr	0.047	1233
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 (%)
1.95-1.9767	0.3264	131	0.268	2663	X-RAY DIFFRACTION	99
1.9767-2.005	0.3087	122	0.2484	2623	X-RAY DIFFRACTION	99
2.005-2.0349	0.3066	127	0.238	2647	X-RAY DIFFRACTION	99
2.0349-2.0667	0.2876	149	0.2277	2696	X-RAY DIFFRACTION	99
2.0667-2.1006	0.252	130	0.218	2633	X-RAY DIFFRACTION	99
2.1006-2.1368	0.2471	147	0.2117	2629	X-RAY DIFFRACTION	99
2.1368-2.1757	0.2725	137	0.2117	2692	X-RAY DIFFRACTION	99
2.1757-2.2175	0.2779	162	0.2015	2571	X-RAY DIFFRACTION	99
2.2175-2.2628	0.2629	144	0.2045	2692	X-RAY DIFFRACTION	99
2.2628-2.312	0.2556	137	0.1985	2685	X-RAY DIFFRACTION	99
2.312-2.3658	0.2622	134	0.1958	2650	X-RAY DIFFRACTION	99
2.3658-2.4249	0.2741	112	0.2009	2704	X-RAY DIFFRACTION	99
2.4249-2.4905	0.2728	142	0.1977	2644	X-RAY DIFFRACTION	99
2.4905-2.5638	0.2378	127	0.1949	2770	X-RAY DIFFRACTION	99
2.5638-2.6465	0.2481	135	0.1905	2638	X-RAY DIFFRACTION	99
2.6465-2.7411	0.2286	124	0.186	2714	X-RAY DIFFRACTION	99
2.7411-2.8509	0.2335	124	0.1875	2676	X-RAY DIFFRACTION	100
2.8509-2.9806	0.2155	170	0.189	2663	X-RAY DIFFRACTION	99
2.9806-3.1378	0.2131	160	0.1889	2676	X-RAY DIFFRACTION	99
3.1378-3.3343	0.2312	132	0.1925	2694	X-RAY DIFFRACTION	99
3.3343-3.5917	0.2241	158	0.1838	2681	X-RAY DIFFRACTION	99
3.5917-3.9531	0.2152	172	0.1734	2673	X-RAY DIFFRACTION	99
3.9531-4.525	0.1843	151	0.1684	2725	X-RAY DIFFRACTION	99
4.525-5.7003	0.2228	165	0.19	2742	X-RAY DIFFRACTION	99
5.7003-59.718	0.2257	116	0.2187	2789	X-RAY DIFFRACTION	96

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	0.4304	-0.0237	0.16	0.2405	-0.3696	0.3365	0.0068	-0.0061	-0.0766	-0.0414	0.008	0.0106	-0.0073	0.0366	-0.0001	0.1253	-0.0118	-0.0046	0.1271	0.0049	0.1516	-8.9127	11.759	71.9797
2	0.7058	0.1542	-0.4129	0.471	-0.2821	0.3661	0.0311	-0.0487	0.1929	0.0079	0.0216	0.1037	-0.1498	-0.0585	0.0003	0.147	0.0061	0.0175	0.1582	0.0072	0.1917	-22.9651	24.9773	81.9788
3	0.5711	0.104	-0.1782	0.1673	-0.1717	0.4573	-0.0261	0.0485	-0.0776	-0.0596	0.0142	-0.0447	0.05	0.065	0	0.1641	-0.0145	-0.0002	0.1343	-0.0216	0.1897	4.5874	11.7754	66.1464
4	0.7821	0.5494	0.0613	0.5353	-0.107	0.6288	0.0153	0.1076	0.0681	-0.0573	0.0459	-0.0363	-0.0531	0.0505	0.0005	0.1697	-0.0138	-0.0003	0.167	0.0247	0.1498	-5.1357	20.7874	52.2785
5	0.489	0.0275	0.0594	0.3149	-0.0609	0.2352	0.0079	-0.0439	0.0874	-0.0407	0.0369	-0.0761	-0.1826	0.2316	-0	0.2	-0.0174	0.0081	0.1801	-0.0139	0.2139	14.8157	18.2325	75.5637
6	0.3551	0.0109	0.0569	0.0497	0.0772	0.0189	-0.0648	-0.2141	-0.011	0.1281	0.0536	-0.0085	-0.2897	0.1058	0.0002	0.1748	0.0022	-0.0093	0.1609	0.0136	0.1482	4.4751	14.5727	86.1836
7	0.4464	-0.0717	0.0296	0.2761	0.1647	0.1759	0.1234	0.0611	-0.0573	-0.1207	-0.0327	-0.1579	0.0591	0.1055	0	0.2091	0.0091	0.0058	0.209	-0.0069	0.1527	-22.9198	33.4033	27.2332
8	0.1123	-0.0886	-0.1428	0.0926	0.0516	0.0689	0.0464	0.3282	-0.1703	-0.249	-0.1054	0.1855	0.2307	-0.0797	0.0007	0.3108	0.0565	-0.0112	0.3175	0.0035	0.1548	-18.3874	30.1671	9.9643
9	0.6747	0.0206	-0.5087	0.1641	-0.0815	0.9049	0.0705	0.1129	0.0494	-0.0444	-0.0444	-0.049	0.0128	0.1607	-0.0001	0.227	0.0268	0.0208	0.2837	0.034	0.2572	-12.7667	38.9709	16.641
10	0.1997	0.0588	-0.3138	0.2304	-0.0246	0.7484	-0.003	0.1534	-0.1816	-0.14	0.0357	0.2416	0.1705	-0.3042	0.0007	0.2843	-0.0252	-0.0421	0.266	0.0049	0.2855	-45.5781	29.4726	24.6609
11	0.1592	0.2062	-0.1625	0.2588	-0.0355	0.2852	-0.0782	0.0767	-0.1466	0.1729	0.0571	-0.1102	0.2034	0.0053	0.0001	0.249	-0.0103	-0.0135	0.2555	0.0199	0.2485	-40.0457	27.6301	34.9225
12	0.4928	-0.2904	0.2946	0.4987	-0.3452	0.8947	0.0677	-0.0921	0.1554	0.0088	-0.0112	0.0754	-0.1491	-0.0142	-0.0001	0.2224	-0.0115	0.014	0.1863	-0.0287	0.2335	-31.5177	43.2283	41.5874
13	0.5455	-0.3834	0.1264	0.3133	0.1185	0.4291	0.0329	0.0009	0.063	0.0002	0.1142	-0.0492	0.1432	0.1263	0	0.1976	-0.0314	-0.0075	0.2417	-0.0352	0.2237	-21.2601	37.4835	44.5464
14	0.1152	-0.226	0.1538	0.2843	-0.137	0.1374	0.047	0.0049	0.0379	-0.126	0.0358	0.1014	-0.0315	-0.4213	-0.0001	0.2545	-0.0016	-0.0261	0.3058	0.025	0.2383	-46.3237	38.3224	23.3162
15	0.3107	-0.1163	-0.2003	0.0658	0.0209	0.22	0.118	0.2411	0.0764	-0.1239	-0.0163	-0.151	-0.0306	-0.2466	0.0002	0.3193	0.0313	-0.0152	0.2569	0.0287	0.1797	-37.6137	34.5178	11.2922

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 158 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 159 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 435 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 436 through 477 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 57 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 58 through 88 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 89 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 245 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 246 through 278 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 279 through 360 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 361 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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