PDB-8t7z: Crystal structure of alpha-glucosidase (yicI) from Klebsiella aer...

ID or keywords:

Entry

Database: PDB / ID: 8t7z

Title

Crystal structure of alpha-glucosidase (yicI) from Klebsiella aerogenes

Components

Alpha-glucosidase yicI

Keywords

HYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / alpha-glucosidase

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700059C	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of alpha-glucosidase (yicI) from Klebsiella aerogenes
Authors: Lovell, S. / Liu, L. / Cooper, A. / Battaile, K.P.

History

Deposition	Jun 21, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8t7z.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb8t7z.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	8t7z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8t7z_validation.pdf.gz	489.4 KB	Display	wwPDB validaton report
Full document	8t7z_full_validation.pdf.gz	532.7 KB	Display
Data in XML	8t7z_validation.xml.gz	142.1 KB	Display
Data in CIF	8t7z_validation.cif.gz	192.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t7/8t7z ftp://data.pdbj.org/pub/pdb/validation_reports/t7/8t7z	HTTPS FTP

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Related structure data

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	#198 - Jun 2016 Beta-galactosidase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Alpha-glucosidase yicI

B: Alpha-glucosidase yicI

C: Alpha-glucosidase yicI

D: Alpha-glucosidase yicI

E: Alpha-glucosidase yicI

F: Alpha-glucosidase yicI

532 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	81.788, 208.509, 280.763
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Alpha-glucosidase yicI Mass: 88650.727 Da / Num. of mol.: 6 / Mutation: H73Q, G79S, D694G, R697N, A699T, L700V, V710A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: EAE_06545 / Plasmid: KlaeA.19615.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FLJ3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Alpha-glucosidase yicI

Mass: 88650.727 Da / Num. of mol.: 6 / Mutation: H73Q, G79S, D694G, R697N, A699T, L700V, V710A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: EAE_06545 / Plasmid: KlaeA.19615.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FLJ3

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.34 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: JCSG+ A7: 20% (w/v) PEG 8000, 100 mM Ches pH 9.5. KlaeA.19615.a.B1.PW39183 at 20.7 mg/mL. plate 13206 well A7 drop 2 . Puck: PSL-0415, Cryo: 20% PEG 200 + 80% crystallant

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 20, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.7→49.55 Å / Num. obs: 132661 / % possible obs: 100 % / Redundancy: 6.9 % / CC_1/2: 0.994 / R_merge(I) obs: 0.185 / R_pim(I) all: 0.076 / R_rim(I) all: 0.2 / Χ²: 1 / Net I/σ(I): 9.4 / Num. measured all: 915751
Reflection shell	Resolution: 2.7→2.75 Å / % possible obs: 100 % / Redundancy: 6.3 % / R_merge(I) obs: 1.169 / Num. measured all: 40706 / Num. unique obs: 6487 / CC_1/2: 0.67 / R_pim(I) all: 0.506 / R_rim(I) all: 1.275 / Χ²: 0.97 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4933: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→29.25 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 27.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2629	6562	4.96 %
R_work	0.2292	-	-
obs	0.2308	132427	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→29.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	36218	0	0	30	36248

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	37285
X-RAY DIFFRACTION	f_angle_d	0.615	50680
X-RAY DIFFRACTION	f_dihedral_angle_d	10.704	13311
X-RAY DIFFRACTION	f_chiral_restr	0.046	5232
X-RAY DIFFRACTION	f_plane_restr	0.005	6622

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 (%)
2.7-2.73	0.3313	219	0.3109	4176	X-RAY DIFFRACTION	100
2.73-2.76	0.3219	211	0.3036	4114	X-RAY DIFFRACTION	100
2.76-2.8	0.3379	229	0.2973	4123	X-RAY DIFFRACTION	100
2.8-2.83	0.3396	186	0.2963	4206	X-RAY DIFFRACTION	100
2.83-2.87	0.3622	217	0.2983	4123	X-RAY DIFFRACTION	100
2.87-2.91	0.3517	212	0.2981	4190	X-RAY DIFFRACTION	100
2.91-2.95	0.3417	250	0.2804	4082	X-RAY DIFFRACTION	100
2.95-2.99	0.2804	202	0.2774	4174	X-RAY DIFFRACTION	100
2.99-3.04	0.296	242	0.2821	4153	X-RAY DIFFRACTION	100
3.04-3.09	0.343	210	0.2759	4125	X-RAY DIFFRACTION	100
3.09-3.14	0.3347	221	0.2629	4207	X-RAY DIFFRACTION	100
3.14-3.2	0.2954	232	0.2708	4092	X-RAY DIFFRACTION	100
3.2-3.26	0.3088	209	0.2545	4227	X-RAY DIFFRACTION	100
3.26-3.33	0.3083	208	0.2489	4137	X-RAY DIFFRACTION	100
3.33-3.4	0.2668	225	0.2486	4182	X-RAY DIFFRACTION	100
3.4-3.48	0.2696	202	0.2365	4163	X-RAY DIFFRACTION	100
3.48-3.57	0.2699	240	0.2221	4194	X-RAY DIFFRACTION	100
3.57-3.66	0.2407	218	0.2149	4149	X-RAY DIFFRACTION	100
3.66-3.77	0.248	208	0.218	4184	X-RAY DIFFRACTION	100
3.77-3.89	0.2523	229	0.2145	4219	X-RAY DIFFRACTION	100
3.89-4.03	0.2464	229	0.2143	4158	X-RAY DIFFRACTION	100
4.03-4.19	0.2293	223	0.2005	4188	X-RAY DIFFRACTION	100
4.19-4.38	0.2234	239	0.1863	4192	X-RAY DIFFRACTION	100
4.38-4.61	0.2135	199	0.1891	4231	X-RAY DIFFRACTION	100
4.61-4.9	0.2198	231	0.1832	4214	X-RAY DIFFRACTION	100
4.9-5.28	0.2474	223	0.1948	4240	X-RAY DIFFRACTION	100
5.28-5.8	0.2515	224	0.2134	4264	X-RAY DIFFRACTION	100
5.8-6.63	0.2421	201	0.2288	4305	X-RAY DIFFRACTION	100
6.63-8.33	0.2492	215	0.2287	4358	X-RAY DIFFRACTION	100
8.33-29.25	0.2354	208	0.226	4495	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	1.0481	-0.2811	0.2635	2.9018	-0.2094	2.8351	-0.0058	0.0542	0.3044	-0.0332	-0.0506	-0.1578	-0.5109	0.0864	0.0098	0.3705	-0.0398	-0.0165	0.3564	-0.0146	0.407	66.4257	125.8677	57.2994
2	1.3816	-0.3913	0.3898	2.6502	0.5386	3.1136	0.0309	-0.0022	-0.0466	-0.0467	-0.0654	0.0272	0.1728	-0.0002	0.0418	0.2014	-0.0106	0.0693	0.2305	0.009	0.2553	56.5812	111.0384	53.3795
3	0.7154	0.0284	-0.2406	1.0159	-0.0272	2.1336	-0.012	-0.0987	-0.1697	-0.0975	-0.1701	-0.1022	0.2126	0.0191	0.1898	0.3548	0.0326	0.0827	0.3606	0.0267	0.4188	67.822	78.4995	57.6573
4	1.6035	0.4756	2.041	1.3441	0.1294	2.7493	0.1026	-0.0083	0.1138	0.0463	-0.2309	-0.1459	0.0876	0.1293	0.1293	0.4365	0.0435	0.1588	0.3198	-0.017	0.3812	62.4782	90.1124	49.727
5	0.9075	-0.063	0.2897	0.8113	-0.1312	0.8453	-0.0858	0.0764	-0.0902	-0.1449	0.0142	-0.0456	0.1187	0.0842	0.069	0.5267	-0.0012	0.0895	0.4099	-0.0463	0.3324	59.5691	90.467	24.6685
6	1.4157	-0.3815	0.4851	1.9507	0.158	2.3253	-0.0426	0.0143	0.1528	-0.2126	-0.1018	0.2925	-0.0894	-0.0453	0.1284	0.3459	0.0149	-0.0177	0.3596	-0.1155	0.4785	33.1388	141.6617	90.4321
7	0.283	0.1716	-0.7066	0.9678	-0.4027	1.6534	-0.016	-0.1163	-0.0191	0.2438	-0.2078	0.2426	0.1522	-0.1438	0.2096	0.3947	-0.053	0.0776	0.5023	-0.1432	0.5037	22.2118	125.597	120.927
8	0.2851	0.339	0.06	1.2549	0.4093	1.1993	0.0272	-0.085	0.0489	0.1642	-0.1462	0.3463	-0.1154	-0.1384	0.1214	0.445	-0.0103	0.0941	0.5374	-0.1658	0.5441	29.3165	145.9538	126.0986
9	0.9839	-0.5851	-0.386	2.3318	-0.0428	1.8965	-0.0672	0.0735	-0.0394	-0.4726	0.1212	-0.1772	0.3438	-0.1285	-0.0255	0.4991	-0.1073	0.1096	0.4155	0.0109	0.4241	60.8486	67.036	81.4649
10	1.5905	-0.378	0.4835	1.3101	-1.1448	3.1105	-0.0204	0.0241	0.0051	0.0583	-0.0786	-0.076	-0.0784	-0.0323	0.0618	0.2659	-0.0748	0.0151	0.2876	-0.0114	0.3615	52.9177	69.3793	96.8657
11	0.783	-0.0019	0.0951	1.2621	-0.3288	1.1391	-0.0182	-0.0103	-0.0381	-0.0388	-0.04	-0.1373	-0.2428	-0.0201	0.0701	0.3419	-0.0441	-0.012	0.3874	0.0187	0.4077	70.6585	86.6029	120.2225
12	1.4789	-0.6481	-0.2224	1.2713	-0.244	1.1508	-0.1456	-0.1296	-0.3011	0.1213	0.0821	-0.0339	0.1602	0.0024	0.051	0.4388	-0.0755	0.0236	0.3553	0.0804	0.4152	57.5864	59.0733	128.789
13	1.3692	0.5744	0.1141	2.6977	-0.6569	2.7208	0.0512	0.0074	-0.1302	0.044	-0.013	0.0488	0.2942	0.1243	-0.0306	0.2822	-0.0031	-0.0005	0.3064	-0.0583	0.2859	25.9224	93.0001	55.7016
14	0.9316	0.0221	0.2269	0.4741	-0.0112	2.1021	0.007	-0.1293	0.2033	0.0428	-0.0026	-0.007	0.0193	-0.0802	-0.0174	0.4187	0.0407	-0.0487	0.4158	-0.112	0.5278	18.4458	129.543	58.4615
15	0.9224	-0.2545	0.1173	0.8339	-0.3164	1.55	-0.0656	0.1559	0.1011	-0.1172	0.0133	0.0133	-0.0556	-0.1069	0.0556	0.3335	-0.0057	-0.0242	0.3263	-0.0441	0.3389	26.9881	121.2616	28.8947
16	1.1838	0.5095	0.4234	3.1572	-0.5564	1.5749	0.1046	-0.0172	-0.1196	0.1163	-0.0754	-0.0653	0.2182	-0.0071	-0.0391	0.3119	-0.0595	0.0218	0.4124	-0.0506	0.2899	62.7561	123.7367	115.5653
17	0.5779	0.5417	0.3161	2.8373	0.7798	1.1568	-0.0455	0.074	0.0433	-0.2037	-0.0002	0.1664	-0.0586	-0.0948	0.0537	0.3423	-0.0615	0.0434	0.46	-0.0314	0.3483	75.9748	137.5484	82.8051
18	0.7366	0.1403	-0.1776	1.9089	0.2498	1.4744	0.0712	-0.0713	0.0785	-0.0726	-0.0831	-0.0346	-0.3265	0.0602	0.0152	0.4065	-0.0877	0.0362	0.3545	-0.0331	0.3188	69.3999	159.4411	104.5902
19	2.0326	0.5829	0.1143	3.2342	-0.3172	1.485	0.1028	-0.1752	0.155	0.1102	-0.134	0.0812	-0.1653	0.0119	0.0013	0.3907	-0.1267	0.0455	0.4138	-0.0326	0.326	27.0212	86.4754	116.1245
20	0.4787	0.7872	-0.146	2.6679	-0.7673	1.2385	0.0731	-0.0433	0.0203	-0.1305	-0.0665	-0.0238	0.0632	-0.1221	-0.0057	0.3095	-0.0759	0.0204	0.4186	-0.018	0.39	12.267	72.4886	84.956
21	1.6466	0.332	0.0658	1.5207	-0.0078	0.8436	0.1654	-0.1743	-0.142	0.0131	-0.0655	-0.0056	0.2261	-0.1731	-0.0896	0.4207	-0.1365	-0.0485	0.3593	0.0484	0.3649	19.92	49.6843	106.0278

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 23 through 132 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 133 through 266 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 267 through 440 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 441 through 528 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 529 through 780 )
6	X-RAY DIFFRACTION	6	chain 'E' and (resid 23 through 234 )
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 235 through 399 )
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 400 through 780 )
9	X-RAY DIFFRACTION	9	chain 'F' and (resid 22 through 113 )
10	X-RAY DIFFRACTION	10	chain 'F' and (resid 114 through 266 )
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 267 through 482 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 483 through 777 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 24 through 266 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 267 through 482 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 483 through 780 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 23 through 266 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 267 through 463 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 464 through 780 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 23 through 266 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 267 through 482 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 483 through 780 )

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