PDB-9jlt: GH57 family amylopullulanase D352N mutant from Aquifex aeolicus c...

ID or keywords:

Entry

Database: PDB / ID: 9jlt

Title

GH57 family amylopullulanase D352N mutant from Aquifex aeolicus complex with alpha-cyclodextrin

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus / cyclodextrin

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-cyclodextrin / 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: 1.56 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

China, 1items

Citation

Journal: J.Struct.Biol. / Year: 2025
Title: Mechanistic insights into cyclodextrins as substrates and inhibitors of GH57 family amylopullulanase from Aquifex aeolicus.
Authors: Zhu, Z. / Li, M. / Xu, Q. / Huang, L. / Zhou, H. / Wang, W. / Wang, Q. / Yu, F.

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	9jlt.cif.gz	415.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9jlt.ent.gz	342 KB	Display	PDB format
PDBx/mmJSON format	9jlt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jlt_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9jlt_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9jlt_validation.xml.gz	45.5 KB	Display
Data in CIF	9jlt_validation.cif.gz	62.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jl/9jlt ftp://data.pdbj.org/pub/pdb/validation_reports/jl/9jlt	HTTPS FTP

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Related structure data

Related structure data	9jluC 9jlvC 9kypC 9kyqC 9kyrC 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
58.7 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
58.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.446, 41.497, 195.485
Angle α, β, γ (deg.)	90.00, 96.46, 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

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

Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin

#3: Chemical

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

Mass: 92.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.16 Å³/Da / Density % sol: 43.13 %
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: May 1, 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: 1.556→97.12 Å / Num. obs: 141554 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC_1/2: 0.994 / R_merge(I) obs: 0.153 / R_rim(I) all: 0.17 / Net I/σ(I): 5.5
Reflection shell	Resolution: 1.56→1.64 Å / R_merge(I) obs: 1.779 / Num. unique obs: 20553 / CC_1/2: 0.444 / R_rim(I) all: 1.976

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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: 1.56→60.216 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2121	6843	4.85 %
R_work	0.1836	-	-
obs	0.185	141121	99.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.56→60.216 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8071	0	180	486	8737

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8498
X-RAY DIFFRACTION	f_angle_d	0.927	11499
X-RAY DIFFRACTION	f_dihedral_angle_d	5.693	5056
X-RAY DIFFRACTION	f_chiral_restr	0.055	1227
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 (%)
1.56-1.5737	0.3313	244	0.3141	4404	X-RAY DIFFRACTION	98
1.5737-1.5922	0.3382	253	0.3174	4334	X-RAY DIFFRACTION	98
1.5922-1.6116	0.317	213	0.2935	4382	X-RAY DIFFRACTION	98
1.6116-1.632	0.3082	230	0.2892	4344	X-RAY DIFFRACTION	99
1.632-1.6535	0.3002	244	0.2783	4448	X-RAY DIFFRACTION	99
1.6535-1.6761	0.2895	216	0.2664	4383	X-RAY DIFFRACTION	99
1.6761-1.7001	0.2845	211	0.2629	4471	X-RAY DIFFRACTION	100
1.7001-1.7255	0.3008	201	0.2557	4497	X-RAY DIFFRACTION	100
1.7255-1.7524	0.2503	190	0.2392	4480	X-RAY DIFFRACTION	100
1.7524-1.7812	0.2614	219	0.2363	4453	X-RAY DIFFRACTION	100
1.7812-1.8119	0.281	221	0.2259	4538	X-RAY DIFFRACTION	100
1.8119-1.8448	0.2154	226	0.2011	4379	X-RAY DIFFRACTION	100
1.8448-1.8803	0.2336	249	0.1906	4495	X-RAY DIFFRACTION	100
1.8803-1.9187	0.2059	222	0.1824	4440	X-RAY DIFFRACTION	100
1.9187-1.9604	0.2044	223	0.1792	4480	X-RAY DIFFRACTION	100
1.9604-2.006	0.2093	248	0.1754	4450	X-RAY DIFFRACTION	100
2.006-2.0562	0.2078	249	0.1821	4469	X-RAY DIFFRACTION	100
2.0562-2.1118	0.2115	225	0.1827	4458	X-RAY DIFFRACTION	100
2.1118-2.1739	0.2063	253	0.1678	4476	X-RAY DIFFRACTION	100
2.1739-2.2441	0.1784	250	0.1629	4446	X-RAY DIFFRACTION	100
2.2441-2.3243	0.2153	249	0.1609	4443	X-RAY DIFFRACTION	100
2.3243-2.4174	0.2039	219	0.1723	4499	X-RAY DIFFRACTION	100
2.4174-2.5274	0.1942	203	0.167	4488	X-RAY DIFFRACTION	100
2.5274-2.6607	0.1996	191	0.1638	4565	X-RAY DIFFRACTION	100
2.6607-2.8274	0.1937	197	0.1608	4534	X-RAY DIFFRACTION	100
2.8274-3.0457	0.1865	254	0.1566	4494	X-RAY DIFFRACTION	100
3.0457-3.3521	0.1944	232	0.1524	4528	X-RAY DIFFRACTION	100
3.3521-3.8371	0.1697	219	0.1447	4610	X-RAY DIFFRACTION	100
3.8371-4.834	0.1716	256	0.1449	4541	X-RAY DIFFRACTION	100
4.834-60.216	0.2091	236	0.1959	4749	X-RAY DIFFRACTION	100

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	1.0303	-0.1003	-0.1789	0.2852	0.1759	0.6683	-0.0695	-0.0764	-0.0974	-0.019	0.061	0.0254	0.0708	-0.1023	0.0178	0.0685	-0.0282	0.0074	0.0562	0.0045	0.1018	-13.3813	14.8167	74.4435
2	1.9965	0.2001	-0.5793	1.4714	-0.0836	4.1327	0.1639	-0.278	0.4064	0.0365	-0.0507	0.0352	-0.552	0.1062	-0.0406	0.1723	-0.0336	0.0354	0.1226	-0.0463	0.177	-22.5509	32.0669	85.3993
3	0.796	0.0858	-0.1588	0.2644	0.0118	0.6679	-0.0293	0.0256	-0.046	-0.011	0.0183	-0.0034	0.059	-0.069	0.0089	0.0762	-0.0342	0.0034	0.0357	0.0051	0.1006	-10.4227	15.0098	74.2949
4	0.944	-0.3174	-0.1862	0.1722	-0.1275	0.5802	0.0086	0.1191	-0.0357	-0.0691	-0.0569	-0.0292	0.0539	0.0767	0.0198	0.1023	-0.0376	0.0132	0.0736	-0.0335	0.1231	5.7788	17.9169	59.9764
5	1.8411	-0.0876	-0.7441	0.9985	0.2988	1.9959	0.0171	0.278	0.0347	-0.1712	0.0596	0.0131	-0.0855	-0.0289	-0.0696	0.1062	-0.0525	-0.0034	0.0892	0.002	0.0935	-8.3265	23.4241	53.0613
6	0.9778	0.0711	0.0479	0.6931	-0.1493	2.5734	-0.0117	-0.1682	0.0726	0.0345	-0.0019	-0.0474	-0.2226	0.0985	0.0406	0.0481	-0.0336	0.0089	0.0959	-0.0231	0.1376	11.5301	20.9426	76.2032
7	4.6712	-0.8642	-0.3724	1.8743	1.1121	3.6223	-0.0406	-0.3607	0.1174	0.004	0.0784	0.0862	-0.0795	-0.0712	-0.0059	0.0296	-0.0241	0.0016	0.1304	-0.0077	0.0863	1.148	17.2855	86.6848
8	1.3091	0.1889	-0.6483	0.4476	-0.2259	0.6741	-0.0333	0.1971	-0.1269	-0.1018	0.0087	-0.0216	0.2218	0.2337	0.0413	0.1765	0.0205	-0.01	0.1639	-0.0229	0.0856	-24.6397	35.0968	22.2131
9	1.6822	-0.1936	-1.2467	1.7319	0.0845	3.8792	0.1634	0.2857	0.3036	-0.1161	-0.1535	0.1052	-0.5984	0.089	-0.0092	0.2908	-0.0028	0.0262	0.2934	0.0644	0.1635	-17.2917	52.0546	9.5659
10	1.2693	0.2179	-0.462	0.3817	-0.2372	1.6007	0.0013	0.1018	-0.0478	-0.0681	0.0093	0.0593	0.1406	0.0316	-0.0054	0.1315	0.0033	-0.0242	0.069	0.0025	0.1151	-32.8533	36.45	29.1412
11	1.4206	0.066	0.0511	1.017	0.115	1.988	0.1115	-0.2541	0.1098	0.0957	-0.0396	0.0262	-0.1425	0.2611	-0.0599	0.126	-0.0468	0.0018	0.1409	-0.0267	0.0946	-26.5118	44.2708	43.9385
12	1.5188	0.155	0.8991	1.2647	0.1167	2.6408	-0.002	0.4157	0.1585	-0.2262	0.1276	0.1759	-0.2962	-0.3534	-0.0094	0.1118	-0.0113	-0.031	0.246	0.0668	0.186	-49.6189	41.2091	24.136
13	3.7395	0.7153	0.1737	2.1192	-0.6941	3.0312	0.0408	0.6062	0.0982	-0.2307	0.0508	0.0081	0.0679	-0.203	-0.0256	0.2571	-0.0332	-0.0463	0.3444	0.015	0.0944	-41.0448	37.3008	12.2557

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 88 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 123 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 124 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 88 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 89 through 123 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 124 through 322 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 323 through 396 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 397 through 435 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 436 through 477 )

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