PDB-6ca3: THE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (G...

ID or keywords:

Entry

Database: PDB / ID: 6ca3

Title

THE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (GH 31) FROM RUMINOCOCCUS OBEUM ATCC 29174 in complex with miglitol

Components

Glycosyl hydrolase, family 31

Glycoside hydrolase

Keywords

HYDROLASE /

structural genomics / PSI-Biology /

protein structure initiative / midwest center for structural genomics / MCSG /

ALPHA-GLUCOSIDASE /

miglitol / Midwest Center for Macromolecular Research / MCMR

Function / homology

Function and homology information

Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds /

carbohydrate binding / carbohydrate metabolic process
Similarity search - Function

Biological species

Blautia obeum ATCC 29174 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.743 Å

Authors

Tan, K. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Macromolecular Research (MCMR)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM094585	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM115586	United States

Citation

Journal: To Be Published
Title: THE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (GH 31) FROM RUMINOCOCCUS OBEUM ATCC 29174 in complex with miglitol
Authors: Tan, K. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Jan 29, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 21, 2021	Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6ca3.cif.gz	561.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6ca3.ent.gz	457.4 KB	Display	PDB format
PDBx/mmJSON format	6ca3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ca/6ca3 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/6ca3	HTTPS FTP

-
Related structure data

Related structure data	6ca1C 3nukS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6c9z-1 6ca1-2 6c9x-2 6c9z-2 6ca1-1 6c9x-1 6acn-d 6q4v-d 4elv-d 2w7o-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: APC106690

-
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: Glycosyl hydrolase, family 31

B: Glycosyl hydrolase, family 31

hetero molecules

155 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycosyl hydrolase, family 31

hetero molecules

defined by author
Evidence: gel filtration
77.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycosyl hydrolase, family 31

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	64.685, 70.826, 88.103
Angle α, β, γ (deg.)	111.32, 107.42, 97.66
Int Tables number	1
Space group name H-M	P1

#1: Protein	Glycosyl hydrolase, family 31 / Glycoside hydrolase Mass: 77426.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blautia obeum ATCC 29174 (bacteria) / Gene: RUMOBE_03919 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic References: UniProt: A5ZY13, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical	ChemComp-MIG / (2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol / Miglitol / Miglitol Mass: 207.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₇NO₅
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1084 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.82 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris, 25% (w/v) PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9191 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9191 Å / Relative weight: 1
Reflection	Resolution: 1.74→32 Å / Num. obs: 131158 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2 % / B_iso Wilson estimate: 23.83 Å² / R_merge(I) obs: 0.053 / R_pim(I) all: 0.053 / R_rim(I) all: 0.074 / Χ²: 1.611 / Net I/σ(I): 21.8
Reflection shell	Resolution: 1.74→1.77 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.594 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6511 / CC_1/2: 0.568 / R_pim(I) all: 0.594 / R_rim(I) all: 0.84 / Χ²: 0.982 / % possible all: 95.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NUK

3nuk

Resolution: 1.743→31.742 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.02

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1911	6603	5.04 %	random
R_work	0.1533	-	-	-
obs	0.1552	131135	95.98 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.743→31.742 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10774	0	34	1084	11892

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	11126
X-RAY DIFFRACTION	f_angle_d	1.042	15030
X-RAY DIFFRACTION	f_dihedral_angle_d	13.746	4101
X-RAY DIFFRACTION	f_chiral_restr	0.078	1524
X-RAY DIFFRACTION	f_plane_restr	0.005	1965

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 (%)
1.7425-1.7623	0.3215	215	0.2753	3894	X-RAY DIFFRACTION	90
1.7623-1.7831	0.373	225	0.2774	4115	X-RAY DIFFRACTION	96
1.7831-1.8048	0.3008	210	0.2565	4164	X-RAY DIFFRACTION	96
1.8048-1.8277	0.2922	223	0.2386	4167	X-RAY DIFFRACTION	96
1.8277-1.8517	0.2839	208	0.2296	4188	X-RAY DIFFRACTION	96
1.8517-1.8771	0.2917	245	0.227	4110	X-RAY DIFFRACTION	96
1.8771-1.9039	0.2747	210	0.215	4199	X-RAY DIFFRACTION	97
1.9039-1.9323	0.2488	203	0.2035	4143	X-RAY DIFFRACTION	96
1.9323-1.9625	0.2487	219	0.1951	4221	X-RAY DIFFRACTION	96
1.9625-1.9947	0.2363	205	0.1832	4142	X-RAY DIFFRACTION	96
1.9947-2.0291	0.2393	204	0.1768	4208	X-RAY DIFFRACTION	97
2.0291-2.0659	0.222	236	0.1778	4140	X-RAY DIFFRACTION	97
2.0659-2.1057	0.2346	220	0.1724	4237	X-RAY DIFFRACTION	97
2.1057-2.1486	0.2215	235	0.1643	4171	X-RAY DIFFRACTION	97
2.1486-2.1954	0.2223	236	0.1655	4123	X-RAY DIFFRACTION	97
2.1954-2.2464	0.2387	222	0.1603	4216	X-RAY DIFFRACTION	97
2.2464-2.3026	0.222	217	0.1609	4186	X-RAY DIFFRACTION	97
2.3026-2.3648	0.1887	230	0.1618	4198	X-RAY DIFFRACTION	97
2.3648-2.4344	0.2407	225	0.1589	4171	X-RAY DIFFRACTION	97
2.4344-2.5129	0.1981	218	0.1518	4191	X-RAY DIFFRACTION	97
2.5129-2.6027	0.194	210	0.1573	4182	X-RAY DIFFRACTION	97
2.6027-2.7068	0.2105	220	0.1611	4164	X-RAY DIFFRACTION	96
2.7068-2.83	0.2022	222	0.1578	4173	X-RAY DIFFRACTION	96
2.83-2.9791	0.1982	228	0.1657	4110	X-RAY DIFFRACTION	95
2.9791-3.1655	0.194	236	0.156	4095	X-RAY DIFFRACTION	96
3.1655-3.4097	0.1884	226	0.1454	4131	X-RAY DIFFRACTION	95
3.4097-3.7523	0.1743	206	0.1359	4073	X-RAY DIFFRACTION	94
3.7523-4.2942	0.1398	229	0.1196	4068	X-RAY DIFFRACTION	94
4.2942-5.4059	0.1335	216	0.1098	4169	X-RAY DIFFRACTION	96
5.4059-31.7477	0.1459	204	0.1431	4183	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	1.9403	0.2864	-0.0267	1.1858	0.152	2.1139	-0.0096	0.2074	-0.1025	-0.0662	0.0568	-0.1226	0.0203	0.0916	-0.0446	0.2035	0.0094	-0.0175	0.2334	-0.0189	0.2006	16.1576	-5.3372	-19.5841
2	0.6101	0.0701	0.1014	0.5992	-0.0482	0.5643	-0.0256	0.234	0.0265	-0.134	0.0524	0.1336	0.0097	-0.1249	-0.0224	0.2431	-0.0246	-0.0292	0.3179	0.0424	0.1998	-13.3131	5.4107	-27.6655
3	0.8783	0.3206	-0.1335	0.995	-0.2091	0.3786	-0.0023	0.1302	-0.1355	-0.0167	0.0156	-0.0286	0.1142	-0.0381	-0.0043	0.3045	-0.0254	-0.0258	0.3187	-0.0449	0.2211	-7.1076	-9.4155	-23.2381
4	0.8302	0.081	0.1942	0.5608	-0.0991	1.1374	-0.0366	0.1011	0.1331	-0.0291	0.0204	0.0499	-0.1432	0.0114	0.0164	0.2126	-0.004	-0.0122	0.1819	0.0345	0.192	3.3195	20.1551	-12.0829
5	1.3643	-0.2364	-0.1124	1.6443	-0.7709	1.4037	-0.0341	-0.2553	0.0748	0.3341	0.1518	0.2583	-0.102	-0.1745	-0.0744	0.2651	0.0499	0.1005	0.2841	-0.0058	0.3119	-20.833	8.3932	27.7908
6	1.2043	-0.1806	0.114	0.8719	-0.2792	0.587	0.0223	0.0366	-0.0417	-0.0161	0.0345	0.0655	0.0028	-0.0409	-0.0488	0.1689	0.0003	0.0217	0.1795	-0.002	0.1615	-4.0147	-1.5238	17.8205
7	2.6887	0.7731	0.3383	1.2878	0.0889	0.9854	-0.0033	0.0235	-0.5707	-0.0296	0.0637	-0.0348	0.2597	-0.0736	-0.043	0.3001	-0.0318	0.0218	0.1829	0.0132	0.2988	-6.9952	-28.0453	20.4513
8	0.5442	0.2002	0.3591	0.6993	0.2539	1.4916	-0.0496	-0.0873	-0.1252	-0.0502	0.0322	0.0874	0.1085	-0.2141	0.0033	0.2663	-0.0336	0.0291	0.2753	0.0416	0.2992	-11.7892	-22.4655	16.1037
9	0.8513	-0.0936	0.1068	0.9457	1.3559	6.1462	0.004	0.0883	-0.1328	-0.2394	0.0222	0.1475	-0.2948	-0.2922	-0.0215	0.3357	-0.0506	-0.0285	0.3255	0.0165	0.3548	-22.3977	-15.7591	2.2764
10	2.2997	0.1878	0.3624	1.3695	-0.14	1.148	0.0274	-0.2331	-0.0679	0.1456	0.0134	0.0938	0.0492	-0.1274	-0.0444	0.2177	-0.0049	0.0489	0.2322	0.0324	0.2348	-8.8534	-12.7603	27.2508
11	1.5237	0.3337	-0.0165	0.8969	-0.3981	1.329	-0.0242	0.058	-0.0724	-0.0584	0.0278	-0.0359	0.0376	0.0253	-0.0034	0.1482	0.0162	0.0002	0.1587	-0.0115	0.129	12.3761	0.7049	15.0094
12	1.3541	0.8168	-0.1166	2.3705	-0.1094	1.3638	0.0773	-0.322	-0.1202	0.1475	-0.0947	-0.1792	-0.0709	0.2277	0.027	0.2273	0.0121	-0.0392	0.3317	0.0134	0.195	19.9648	-1.7101	33.562

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 139 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 140 through 299 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 300 through 412 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 413 through 663 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -1 through 43 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 44 through 200 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 201 through 282 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 283 through 332 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 333 through 366 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 367 through 412 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 413 through 608 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 609 through 663 )

-
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