PDB-9kyq: GH57 family amylopullulanase from Aquifex aeolicus wild type co-c...

ID or keywords:

Entry

Database: PDB / ID: 9kyq

Title

GH57 family amylopullulanase from Aquifex aeolicus wild type co-crystallize with gama-cyclodextrin

Components

(Glycoside hydrolase family 57 N-terminal domain-containing ...) x 2

Keywords

HYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus

Function / homology

Function and homology information

catalytic activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Aquifex aeolicus VF5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Zhu, Z.M. / Wang, W.W. / Yu, F. / Li, M.J. / Xu, Q. / Zhou, H. / Huang, L.Q. / Wang, Q.S.

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	Dec 9, 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	9kyq.cif.gz	424.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9kyq.ent.gz	347.1 KB	Display	PDB format
PDBx/mmJSON format	9kyq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kyq_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9kyq_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9kyq_validation.xml.gz	50.3 KB	Display
Data in CIF	9kyq_validation.cif.gz	69.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ky/9kyq ftp://data.pdbj.org/pub/pdb/validation_reports/ky/9kyq	HTTPS FTP

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Related structure data

Related structure data	9jltC 9jluC 9jlvC 9kypC 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

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
Evidence: native gel electrophoresis
58.3 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
58.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.450, 41.350, 194.020
Angle α, β, γ (deg.)	90.00, 96.24, 90.00
Int Tables number	3
Space group name H-M	P121

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Glycoside hydrolase family 57 N-terminal domain-containing ... , 2 types, 2 molecules AB

#1: Protein	Glycoside hydrolase family 57 N-terminal domain-containing protein / GH57 family amylopullulanase Mass: 57253.234 Da / Num. of mol.: 1 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: Protein	Glycoside hydrolase family 57 N-terminal domain-containing protein / GH57 family amylopullulanase Mass: 57391.383 Da / Num. of mol.: 1 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 , 1 types, 2 molecules

#3: Polysaccharide

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

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 725 molecules

#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.14 Å³/Da / Density % sol: 42.45 %
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 9M / Detector: PIXEL / Date: Nov 10, 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: 1.6→64.29 Å / Num. obs: 128326 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC_1/2: 0.996 / R_merge(I) obs: 0.132 / R_pim(I) all: 0.057 / R_rim(I) all: 0.144 / Χ²: 0.97 / Net I/σ(I): 9.5 / Num. measured all: 813928
Reflection shell	Resolution: 1.6→1.64 Å / % possible obs: 99.7 % / Redundancy: 5.3 % / R_merge(I) obs: 1.444 / Num. measured all: 49612 / Num. unique obs: 9430 / CC_1/2: 0.445 / R_pim(I) all: 0.691 / R_rim(I) all: 1.607 / Χ²: 0.84 / 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: 1.6→64.29 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1988	6251	4.87 %
R_work	0.1696	-	-
obs	0.171	128280	99.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→64.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8053	0	117	716	8886

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8468
X-RAY DIFFRACTION	f_angle_d	0.937	11463
X-RAY DIFFRACTION	f_dihedral_angle_d	6.312	7043
X-RAY DIFFRACTION	f_chiral_restr	0.067	1208
X-RAY DIFFRACTION	f_plane_restr	0.006	1439

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 (%)
1.6-1.6182	0.3016	194	0.3041	4026	X-RAY DIFFRACTION	99
1.6182-1.6372	0.278	203	0.2806	4006	X-RAY DIFFRACTION	100
1.6372-1.6572	0.2857	221	0.2674	4105	X-RAY DIFFRACTION	100
1.6572-1.6782	0.293	191	0.2476	3983	X-RAY DIFFRACTION	100
1.6782-1.7003	0.2558	212	0.243	4034	X-RAY DIFFRACTION	100
1.7003-1.7236	0.2885	236	0.2518	4079	X-RAY DIFFRACTION	100
1.7236-1.7482	0.2815	208	0.2522	4006	X-RAY DIFFRACTION	100
1.7482-1.7743	0.2674	194	0.2339	4050	X-RAY DIFFRACTION	100
1.7743-1.802	0.2519	218	0.2195	4111	X-RAY DIFFRACTION	100
1.802-1.8315	0.224	205	0.2023	3947	X-RAY DIFFRACTION	100
1.8315-1.8631	0.234	219	0.1906	4117	X-RAY DIFFRACTION	100
1.8631-1.897	0.2134	206	0.186	4068	X-RAY DIFFRACTION	100
1.897-1.9335	0.2247	189	0.1777	4002	X-RAY DIFFRACTION	99
1.9335-1.973	0.1961	213	0.1785	4085	X-RAY DIFFRACTION	100
1.973-2.0159	0.2036	203	0.1759	4019	X-RAY DIFFRACTION	100
2.0159-2.0628	0.2194	220	0.179	4125	X-RAY DIFFRACTION	100
2.0628-2.1144	0.2083	214	0.1692	4008	X-RAY DIFFRACTION	99
2.1144-2.1715	0.1958	222	0.165	4046	X-RAY DIFFRACTION	99
2.1715-2.2354	0.2077	226	0.1632	4006	X-RAY DIFFRACTION	99
2.2354-2.3076	0.1972	191	0.1663	4108	X-RAY DIFFRACTION	99
2.3076-2.3901	0.2014	209	0.1694	4051	X-RAY DIFFRACTION	99
2.3901-2.4858	0.2098	215	0.1685	4042	X-RAY DIFFRACTION	100
2.4858-2.5989	0.1982	199	0.1681	4077	X-RAY DIFFRACTION	99
2.5989-2.7359	0.1772	196	0.1596	4098	X-RAY DIFFRACTION	99
2.7359-2.9073	0.1841	234	0.1582	4012	X-RAY DIFFRACTION	99
2.9073-3.1318	0.1828	216	0.1551	4081	X-RAY DIFFRACTION	99
3.1318-3.447	0.1807	178	0.1514	4145	X-RAY DIFFRACTION	99
3.447-3.9457	0.1515	167	0.1339	4144	X-RAY DIFFRACTION	99
3.9457-4.9709	0.1446	237	0.1309	4164	X-RAY DIFFRACTION	100
4.9709-64.29	0.2172	215	0.1753	4284	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	1.8684	0.7825	-0.3444	0.6338	-0.1205	1.6757	0.0107	-0.0936	0.0105	0.0017	-0.0326	0.0595	0.0404	-0.0929	-0.001	0.1619	0.0308	-0.0023	0.1294	-0.0035	0.1657	-41.184	36.2978	39.1056
2	1.3067	0.0088	-0.4632	0.9039	-0.2424	2.7863	0.0489	-0.1726	0.0753	0.1132	-0.0154	-0.0255	-0.1711	0.2094	-0.029	0.1936	0.0027	-0.0192	0.1742	-0.0339	0.1683	-26.3673	42.0787	43.6507
3	1.1126	0.0246	-0.1335	1.2189	-0.3872	3.2713	0.004	0.2663	0.1059	-0.0998	0.0195	0.1278	-0.2252	-0.3846	-0.0183	0.1553	0.0209	-0.0136	0.2337	0.0163	0.2334	-49.47	39.2021	24.0717
4	3.8779	0.8849	-0.2173	1.9205	-0.4488	3.0818	-0.0541	0.5114	0.0238	-0.2586	0.068	0.0591	0.0565	-0.1947	-0.0061	0.1898	0.0196	-0.0321	0.2807	-0	0.127	-41.0228	34.9334	12.2175
5	2	-4.9044	-8.7037	2	8.5034	2	-0.1225	1.1256	3.1581	1.7004	1.056	0.3652	-0.6497	-0.6047	-0.8991	0.7251	-0.0092	0.0027	0.658	-0.0351	0.5524	-44.507	17.7662	4.6804
6	0.8267	0.0756	-0.2773	0.52	-0.1823	1.314	-0.0087	-0.0119	-0.0722	-0.0205	0.0191	0.0328	0.0854	-0.0251	-0.005	0.1241	-0.0091	0.0068	0.0983	-0.007	0.1533	-10.5736	12.7038	69.8233
7	1.2386	-0.7967	-0.6917	0.799	-0.1184	1.7357	-0.0082	-0.2529	0.0082	0.0935	-0.0211	-0.0049	-0.0136	0.0549	0.0353	0.1388	-0.0072	-0.0073	0.2188	-0.0108	0.141	-20.4299	19.2022	89.198
8	2.3341	-0.1718	-1.6327	1.056	0.2178	3.0518	0.1512	0.0282	0.3402	-0.0133	-0.0348	0.0762	-0.3858	-0.2445	-0.0857	0.1585	0.0208	0.0207	0.1631	0.0037	0.2303	-27.5389	26.4713	78.6224
9	0.6103	-0.0927	-0.0363	0.1888	-0.0053	0.6362	-0.0142	0.0434	-0.0409	-0.03	0.0048	-0.0292	0.044	0.0737	0.0177	0.1246	-0.0088	0.0112	0.0825	-0.0109	0.1355	1.4599	12.4716	66.4314
10	1.7116	-0.1958	-0.7742	0.9585	0.2924	2.7139	0.0191	0.2028	0.0413	-0.1672	0.029	0.0642	-0.1023	-0.0086	-0.0566	0.1498	-0.0306	-0.01	0.1242	0.0082	0.1401	-8.0362	21.4673	52.5975
11	1.2244	0.1012	-0.0889	0.7749	0.0849	2.7326	0.0221	-0.1351	0.1442	0.0212	-0.042	-0.003	-0.1996	0.1773	0.0103	0.1004	-0.0078	0.0039	0.1532	-0.0142	0.2	11.8719	19.0934	75.6662
12	4.0456	-1.441	-0.0147	2.7844	-0.1662	2.7431	-0.0669	-0.3907	0.0268	0.1638	0.0412	0.0412	-0.0155	-0.0251	0.021	0.1069	-0.0212	0.0002	0.1896	-0.0204	0.1211	1.7519	15.1115	86.125
13	0.8789	-0.0058	-0.6334	0.8317	0.2168	2.1998	-0.0028	0.0248	-0.0745	-0.0153	0.024	-0.0383	0.1956	0.1908	-0.008	0.1738	0.0317	-0.0082	0.1527	-0.0106	0.167	-26.3386	32.93	26.991
14	1.0633	0.5922	-0.8896	0.7352	0.1632	1.8255	-0.0272	0.3615	0.0199	-0.136	0.0031	0.057	-0.0166	0.0441	0.0068	0.2478	0	-0.0356	0.3952	0.0072	0.2176	-19.8743	39.098	5.5832
15	4.7183	0.3474	-3.2872	2.3871	-0.3862	4.5396	0.5008	0.2293	0.8358	0.1455	-0.0564	-0.1396	-1.1157	0.0817	-0.3594	0.368	-0.0339	0.0573	0.3062	0.0514	0.3479	-14.1141	52.5209	12.4605
16	1.4903	0.3766	-0.9528	0.6094	-0.5391	2.0149	-0.0437	-0.031	-0.0608	-0.0409	-0.0377	-0.0956	0.1317	0.4694	0.1051	0.1904	0.0495	-0.0154	0.2843	-0.0271	0.1745	-12.9483	35.1308	20.5705
17	2.8894	-0.9959	-0.1014	1.8405	-0.1076	1.7371	-0.0168	0.1204	-0.1871	-0.0493	0.0492	0.2536	0.1924	-0.3095	-0.0321	0.193	-0.0365	-0.016	0.1881	-0.0117	0.1712	-47.6061	30.1183	25.1085

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 246 through 322 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 323 through 396 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 397 through 435 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 436 through 477 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 478 through 478 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 2 through 68 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 69 through 102 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 103 through 158 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 159 through 322 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 323 through 396 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 397 through 435 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 436 through 477 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 68 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 69 through 102 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 103 through 123 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 124 through 194 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 195 through 245 )

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Glycoside hydrolase family 57 N-terminal domain-containing ... , 2 types, 2 molecules AB

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Non-polymers , 4 types, 725 molecules

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Glycoside hydrolase family 57 N-terminal domain-containing ... , 2 types, 2 molecules AB

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Sugars , 1 types, 2 molecules

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Non-polymers , 4 types, 725 molecules

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