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

ID or keywords:

Entry

Database: PDB / ID: 9jlr

Title

Crystal structure of GH57 family amylopullulanase from Aquifex aeolicus mutant E256Q in complex with maltopentaose

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 / alpha-maltopentaose / 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: 2.79 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: 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

-
Download

PDBx/mmCIF format	9jlr.cif.gz	810.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9jlr.ent.gz	680 KB	Display	PDB format
PDBx/mmJSON format	9jlr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9jlr_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	9jlr_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9jlr_validation.xml.gz	76.9 KB	Display
Data in CIF	9jlr_validation.cif.gz	98.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jl/9jlr ftp://data.pdbj.org/pub/pdb/validation_reports/jl/9jlr	HTTPS FTP

-
Related structure data

Related structure data	9jlqC 9jlsC 9jlwC 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

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

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

hetero molecules

237 kDa, 4 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
59.2 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
59.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

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

hetero molecules

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

4

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.170, 165.170, 98.010
Angle α, β, γ (deg.)	90.00, 109.46, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Glycoside hydrolase family 57 N-terminal domain-containing protein

Mass: 58323.418 Da / Num. of mol.: 4 / 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

#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.: 4
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: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.38 Å³/Da / Density % sol: 48.41 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 45% MPD, 5% PEG8000, 0.1 M MES 6.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection	Resolution: 2.79→62.92 Å / Num. obs: 52825 / % possible obs: 98.4 % / Redundancy: 6.9 % / CC_1/2: 0.99 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.79→2.86 Å / R_merge(I) obs: 1.687 / Num. unique obs: 3869 / CC_1/2: 0.391 / R_rim(I) all: 1.816

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.79→46.01 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2446	2612	4.95 %
R_work	0.188	-	-
obs	0.1907	52769	98.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.79→46.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16352	0	224	51	16627

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	17039
X-RAY DIFFRACTION	f_angle_d	0.799	23051
X-RAY DIFFRACTION	f_dihedral_angle_d	7.15	2259
X-RAY DIFFRACTION	f_chiral_restr	0.058	2457
X-RAY DIFFRACTION	f_plane_restr	0.006	2880

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 (%)
2.79-2.84	0.3772	158	0.3232	2596	X-RAY DIFFRACTION	99
2.84-2.9	0.3863	123	0.308	2638	X-RAY DIFFRACTION	97
2.9-2.95	0.3653	163	0.2861	2612	X-RAY DIFFRACTION	99
2.95-3.02	0.3065	146	0.2605	2576	X-RAY DIFFRACTION	97
3.02-3.09	0.2843	148	0.2492	2622	X-RAY DIFFRACTION	99
3.09-3.17	0.3146	147	0.2365	2631	X-RAY DIFFRACTION	98
3.17-3.25	0.2888	161	0.2265	2626	X-RAY DIFFRACTION	99
3.25-3.35	0.318	144	0.2282	2609	X-RAY DIFFRACTION	98
3.35-3.46	0.3072	123	0.2075	2667	X-RAY DIFFRACTION	98
3.46-3.58	0.2473	143	0.1956	2622	X-RAY DIFFRACTION	99
3.58-3.72	0.2595	123	0.1837	2674	X-RAY DIFFRACTION	98
3.72-3.89	0.2389	130	0.1837	2635	X-RAY DIFFRACTION	99
3.89-4.1	0.2199	155	0.179	2627	X-RAY DIFFRACTION	98
4.1-4.35	0.2309	141	0.1632	2650	X-RAY DIFFRACTION	99
4.35-4.69	0.1879	116	0.1523	2682	X-RAY DIFFRACTION	98
4.69-5.16	0.2334	122	0.1651	2683	X-RAY DIFFRACTION	98
5.16-5.9	0.2412	141	0.1744	2658	X-RAY DIFFRACTION	99
5.91-7.43	0.2242	103	0.1945	2673	X-RAY DIFFRACTION	98
7.44-46.01	0.1557	125	0.1365	2676	X-RAY DIFFRACTION	97

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	2.6204	0.2513	0.294	0.7516	0.0004	1.4244	-0.0507	-0.0617	0.0238	0.0818	0.0626	-0.1803	0.0908	0.2771	0.0208	0.4272	-0.01	-0.0021	0.4166	-0.0155	0.4367	26.9449	0.598	13.9122
2	1.2723	0.4654	-0.0014	1.245	0.4415	2.0185	-0.0395	0.2237	-0.144	-0.2162	0.1013	0.0524	0.0945	-0.1644	-0.0159	0.4486	-0.0419	0.0404	0.433	0.0071	0.4795	2.07	-3.425	0.1415
3	4.1441	1.073	0.1854	1.8857	-0.6696	1.9527	-0.0395	-0.2351	0.1901	-0.0185	-0.1658	-0.1586	-0.1509	-0.1515	0.2124	0.4286	0.0179	0.0305	0.4248	-0.0305	0.4573	1.982	8.1833	17.8993
4	2.2555	-1.4788	-0.4828	2.569	0.9239	2.3825	-0.0644	0.4231	0.2869	-0.5935	0.1608	-0.3208	-0.4026	0.0534	-0.0104	0.5098	-0.087	0.0042	0.4815	-0.0041	0.5124	7.905	-0.1223	-11.0222
5	7.3668	0.5379	0.3629	2.0393	0.9058	8.1431	-0.1385	0.1619	0.7298	-0.2097	0.1084	-0.1261	-0.3552	-0.0689	0.0419	0.4416	-0.0345	0.0849	0.5976	-0.003	0.532	21.9859	-4.767	-8.5039
6	4.4635	0.593	-0.7103	1.0029	0.0062	0.413	-0.1861	-0.5123	0.2594	0.0673	0.2212	0.2148	-0.2394	-0.2829	-0.0562	0.3587	0.012	0.0144	0.4262	0.029	0.4996	-18.5832	43.0749	26.7779
7	5.5827	0.3103	-0.1524	1.009	0.4559	0.8857	0.1525	-0.4097	-1.3612	-0.1453	0.061	0.2703	0.1783	0.0248	0.0061	0.55	0.0118	0.0043	0.5951	0.0718	0.848	-34.5098	27.3173	27.5128
8	4.0026	0.5405	-0.0026	0.7793	0.1522	0.6747	0.0941	-0.7753	0.1957	0.1966	-0.0875	0.189	-0.1019	-0.1425	-0.0418	0.4785	0.0152	0.0049	0.6166	-0.0199	0.4975	-24.3118	42.0626	34.1948
9	2.6124	0.1847	0.436	1.584	0.1784	1.7416	0.02	-0.0252	-0.1348	-0.0689	0.0898	0.026	-0.1108	0.107	-0.0305	0.3767	-0.0194	0.0057	0.3679	0.0248	0.4829	0.5078	37.6328	19.6247
10	3.2675	-0.2591	-0.1222	0.8138	-0.4558	2.4206	-0.1287	-0.1658	-0.1586	-0.0827	-0.0587	0.1223	0.3248	0.036	0.0203	0.4869	-0.0059	0.0151	0.3187	-0.0107	0.4592	-2.4559	36.0886	21.6541
11	6.4639	-1.3314	0.3056	3.7121	0.0629	6.4218	-0.2767	0.0679	-0.2093	0.0874	0.2612	0.4162	0.1046	-0.4937	0.0128	0.5139	-0.0467	-0.0121	0.6124	-0.0297	0.388	-20.0079	40.9201	6.8785
12	2.6046	0.612	0.6696	1.8251	-0.2516	1.6849	-0.0403	0.3205	-0.0466	-0.1537	0.2233	0.3187	0.1677	-0.6553	-0.121	0.6011	-0.0558	-0.075	0.8087	0.0888	0.522	3.6854	-9.7166	48.6283
13	2.001	0.0457	0.128	1.1923	-0.6766	2.7519	0.0389	0.1375	0.2017	-0.0142	0.0393	-0.0854	-0.3786	0.1164	-0.1274	0.5197	-0.0407	-0.0163	0.4634	-0.018	0.4892	24.8618	-0.1479	59.8987
14	2.8367	1.713	1.6969	5.638	-2.4279	3.4815	-0.3187	-0.2156	0.1227	-0.4446	0.323	-0.0303	-0.531	-0.2594	0.0758	0.536	-0.0445	-0.01	0.6929	0.0306	0.404	11.7823	-18.8057	69.5056
15	3.252	1.3304	-0.7708	2.0048	0.2738	1.4612	-0.1795	0.1235	0.0575	-0.4153	0.189	-0.2219	0.1586	0.2542	-0.0575	0.6777	0.0226	0.0734	0.6561	0.051	0.4932	4.0941	46.8866	65.0183
16	2.1786	0.1736	-0.3429	1.0709	-0.1279	1.3285	-0.2289	0.3829	-0.0252	-0.2252	-0.0337	0.0379	0.0509	-0.2266	0.0986	0.5679	-0.0014	0.0014	0.5517	0.0312	0.4785	-16.8488	45.7471	73.3231
17	2.4962	-0.0342	-0.8045	1.7687	0.1719	2.6677	-0.1132	0.3416	-0.4321	-0.3144	-0.0029	-0.1957	0.4762	-0.1734	0.1423	0.7918	-0.0464	0.1044	0.5958	-0.0031	0.6219	-13.4672	25.5524	69.2586
18	2.6198	0.797	0.8826	3.9534	-0.0305	2.73	0.226	-0.1503	-0.3161	0.3106	0.0914	0.0427	0.4631	-0.1229	-0.1373	0.6452	0.021	0.0317	0.5775	0.0555	0.3791	-17.0953	34.496	86.0272
19	1.9988	-0.0682	0.025	5.5053	-1.0581	2.9273	-0.0303	-0.223	0.0249	0.6568	0.0248	-0.3924	-0.3311	0.0783	0.0031	0.5752	0.0238	-0.0044	0.5209	-0.0402	0.3905	-12.4344	55.8659	89.5295
20	2.432	1.1578	-0.9291	4.7793	1.9378	3.6159	0.0395	-0.2848	0.2626	-0.1723	0.1688	-0.7857	0.2745	0.4219	-0.2543	0.4542	-0.0478	0.105	0.6089	0.0394	0.6355	-6.1722	58.4614	84.5471

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 185 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 186 through 322 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 323 through 396 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 397 through 435 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 436 through 477 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 88 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 89 through 123 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 124 through 200 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 201 through 360 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 361 through 434 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 435 through 477 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 185 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 186 through 444 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 445 through 484 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 158 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 159 through 278 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 279 through 396 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 397 through 419 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 420 through 444 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 445 through 485 )

-
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