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

ID or keywords:

Entry

Database: PDB / ID: 9jlv

Title

Crystal structure of GH57 family amylopullulanase from Aquifex aeolicus mutant E256Q in complex with alpha-cyclodextrin

Components

Glycoside hydrolase family 57 N-terminal domain-containing protein

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus / alpha-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 / CITRATE ANION / 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: 1.51 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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PDBx/mmCIF format	9jlv.cif.gz	222.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9jlv_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9jlv_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9jlv_validation.xml.gz	26.9 KB	Display
Data in CIF	9jlv_validation.cif.gz	37.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jl/9jlv ftp://data.pdbj.org/pub/pdb/validation_reports/jl/9jlv	HTTPS FTP

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Related structure data

Related structure data	9jltC 9jluC 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) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

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Related items in Molecule of the Month

#203 - Nov 2016
Aminopeptidase 1 and Autophagy
similarity (2)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Glycoside hydrolase family 57 N-terminal domain-containing protein

hetero molecules

59.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	199.970, 40.570, 62.620
Angle α, β, γ (deg.)	90.00, 102.82, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 1 molecules A

#1: Protein	Glycoside hydrolase family 57 N-terminal domain-containing protein Mass: 57252.250 Da / Num. of mol.: 1 / Mutation: E256Q 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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide

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

Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}	LINUCS	PDB-CARE

#3: Polysaccharide

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

Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 344 molecules

#4: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅O₇
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 43.14 %
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: BL10U2 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 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: 1.51→28.58 Å / Num. obs: 76826 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.062 / R_pim(I) all: 0.027 / R_rim(I) all: 0.067 / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.51→1.55 Å / R_merge(I) obs: 0.781 / Num. unique obs: 5334 / CC_1/2: 0.515 / R_pim(I) all: 0.483 / R_rim(I) all: 0.925

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
xia2		data scaling
xia2		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.51→25.218 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.184	3885	5.06 %
R_work	0.164	-	-
obs	0.165	76794	99.17 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.51→25.218 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4052	0	149	340	4541

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4335
X-RAY DIFFRACTION	f_angle_d	0.918	5881
X-RAY DIFFRACTION	f_dihedral_angle_d	5.609	3614
X-RAY DIFFRACTION	f_chiral_restr	0.052	639
X-RAY DIFFRACTION	f_plane_restr	0.006	724

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 (%)
1.51-1.5284	0.2736	110	0.2736	2422	X-RAY DIFFRACTION	92
1.5284-1.5478	0.2713	114	0.2614	2488	X-RAY DIFFRACTION	94
1.5478-1.5681	0.2768	130	0.257	2499	X-RAY DIFFRACTION	96
1.5681-1.5896	0.2838	137	0.2357	2493	X-RAY DIFFRACTION	97
1.5896-1.6123	0.2866	122	0.2154	2643	X-RAY DIFFRACTION	100
1.6123-1.6364	0.2184	137	0.2094	2578	X-RAY DIFFRACTION	100
1.6364-1.6619	0.2405	139	0.2015	2618	X-RAY DIFFRACTION	100
1.6619-1.6892	0.2256	150	0.1938	2611	X-RAY DIFFRACTION	100
1.6892-1.7183	0.2303	123	0.1879	2575	X-RAY DIFFRACTION	100
1.7183-1.7495	0.2008	146	0.1806	2619	X-RAY DIFFRACTION	100
1.7495-1.7832	0.2293	159	0.1739	2598	X-RAY DIFFRACTION	100
1.7832-1.8196	0.1842	114	0.1675	2640	X-RAY DIFFRACTION	100
1.8196-1.8591	0.1967	139	0.1581	2628	X-RAY DIFFRACTION	100
1.8591-1.9024	0.2015	135	0.1631	2610	X-RAY DIFFRACTION	100
1.9024-1.9499	0.205	126	0.1724	2617	X-RAY DIFFRACTION	100
1.9499-2.0026	0.1767	161	0.1561	2601	X-RAY DIFFRACTION	100
2.0026-2.0615	0.1778	160	0.1577	2587	X-RAY DIFFRACTION	100
2.0615-2.128	0.159	134	0.1536	2659	X-RAY DIFFRACTION	100
2.128-2.204	0.1932	151	0.1542	2568	X-RAY DIFFRACTION	100
2.204-2.2922	0.1762	119	0.1583	2632	X-RAY DIFFRACTION	100
2.2922-2.3965	0.1659	147	0.1612	2657	X-RAY DIFFRACTION	100
2.3965-2.5227	0.1908	147	0.1605	2607	X-RAY DIFFRACTION	100
2.5227-2.6806	0.1578	137	0.1542	2646	X-RAY DIFFRACTION	100
2.6806-2.8873	0.1998	156	0.1579	2612	X-RAY DIFFRACTION	100
2.8873-3.1774	0.1645	124	0.1602	2660	X-RAY DIFFRACTION	100
3.1774-3.6359	0.1705	158	0.1506	2649	X-RAY DIFFRACTION	100
3.6359-4.5764	0.1666	153	0.1363	2653	X-RAY DIFFRACTION	100
4.5764-25.218	0.1632	157	0.1632	2739	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	1.2123	-0.137	0.0071	0.7156	-0.0512	1.4859	0.0051	-0.0818	-0.0466	0.0521	0.0182	-0.0267	0.0753	0.0929	-0.047	0.0954	0.0009	0.0027	0.0652	0.0091	0.0842	-32.614	15.4348	28.1985
2	2.9785	-0.7853	0.8977	1.5994	-0.2652	2.7569	-0.186	-0.2656	0.2797	0.085	0.109	-0.1767	-0.2481	0.399	0.0618	0.1871	-0.0226	-0.0326	0.26	-0.0347	0.183	-17.7843	28.8991	41.8885
3	1.5812	0.2706	0.9116	0.794	0.4276	2.2159	0.0065	-0.2738	-0.0786	0.1701	0.0092	-0.0246	0.0807	0.0316	-0.0112	0.161	0.0383	0.0157	0.1797	0.021	0.1094	-31.0169	18.0419	43.2768
4	1.2036	0.0349	-0.2121	0.7934	-0.2307	1.5715	0.0128	0.1001	-0.0952	-0.078	-0.0085	0.0461	0.0973	0.0655	-0.0098	0.1096	-0.0002	-0.0162	0.0755	-0.0116	0.1134	-32.6484	13.0894	8.3079
5	1.1817	-0.0222	0.3279	1.7103	0.829	2.4527	0.0456	0.0535	0.045	0.0567	-0.0255	-0.0392	-0.0815	-0.1286	-0.0146	0.1004	0.0062	-0.0052	0.0625	0.0178	0.1115	-43.7725	27.5945	10.237
6	1.9816	-0.0729	1.1238	0.6393	-0.144	2.2625	-0.0909	-0.1127	0.1224	0.0562	0.1002	0.099	-0.3543	-0.308	0.0497	0.1762	0.0495	0.0122	0.1321	0.0198	0.1482	-47.4721	31.0416	21.1422
7	2.1451	-0.3749	0.9019	0.7522	-0.2981	2.5833	-0.046	-0.2031	-0.0562	0.0209	0.0599	0.1509	-0.0236	-0.5075	-0.0208	0.1226	0.0206	0.0297	0.1728	0.0346	0.1629	-51.8598	23.4953	23.8466
8	2.4624	-0.16	0.5837	1.0173	-0.0777	1.5237	-0.0229	0.1022	0.1416	-0.0646	-0.0081	-0.0887	-0.1373	0.3125	0.0357	0.1585	-0.0228	0.0173	0.1512	0.0075	0.0971	-24.567	22.2695	5.6213
9	2.9265	-0.2782	0.4617	2.0801	0.164	2.8759	-0.0131	-0.044	0.0289	0.0391	0.0114	-0.1198	-0.0582	0.3793	-0.0264	0.1134	-0.0054	0.0101	0.2356	0.0093	0.1393	-16.1016	16.6024	17.0055

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 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 278 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 279 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 )

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