PDB-6c9z: THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (GH 31) W169Y muta...

ID or keywords:

Entry

Database: PDB / ID: 6c9z

Title

THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (GH 31) W169Y mutant FROM RUMINOCOCCUS OBEUM ATCC 29174 in complex with voglibose

Components

Glycosyl hydrolase, family 31

Glycoside hydrolase

Keywords

HYDROLASE /

structural genomics / PSI-Biology /

protein structure initiative / midwest center f or structural genomics / MCSG /

alpha-Glucosidase /

voglibose / 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: 2.101 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 alpha-Glucosidase (GH 31) W169Y mutant FROM RUMINOCOCCUS OBEUM ATCC 29174 in complex with voglibose
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	6c9z.cif.gz	542.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6c9z.ent.gz	446.2 KB	Display	PDB format
PDBx/mmJSON format	6c9z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9z ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9z	HTTPS FTP

-
Related structure data

Related structure data	3nukS S: Starting model for refinement
Similar structure data	6ca3-1 6ca1-1 6c9x-1 6ca1-2 6ca3-2 6c9x-2 6acn-d 3ojs-d 2cvx-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
77.7 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)	67.751, 126.346, 88.191
Angle α, β, γ (deg.)	90.00, 107.82, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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-VOG / (1S,2S,3R,4S,5S)-5-[(1,3-dihydroxypropan-2-yl)amino]-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol / voglibose / Voglibose Mass: 267.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₁NO₇ / Comment: inhibitor*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris 25% (w/v) PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013 / Details: mirror
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.1→33.5 Å / Num. obs: 79048 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 34.04 Å² / R_merge(I) obs: 0.102 / Net I/σ(I): 20.7
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3701 / % possible all: 92.9

-
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: 2.101→32.25 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.53

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2458	3924	4.98 %	Random
R_work	0.1918	-	-	-
obs	0.1945	78852	96.07 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.101→32.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10712	0	36	263	11011

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	11032
X-RAY DIFFRACTION	f_angle_d	1.011	14911
X-RAY DIFFRACTION	f_dihedral_angle_d	13.799	4045
X-RAY DIFFRACTION	f_chiral_restr	0.074	1519
X-RAY DIFFRACTION	f_plane_restr	0.004	1952

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 (%)
2.1015-2.1271	0.3743	87	0.2973	1617	X-RAY DIFFRACTION	58
2.1271-2.154	0.4444	136	0.3505	2573	X-RAY DIFFRACTION	93
2.154-2.1823	0.4344	119	0.3483	2618	X-RAY DIFFRACTION	93
2.1823-2.2122	0.3343	126	0.3318	2660	X-RAY DIFFRACTION	95
2.2122-2.2438	0.4087	138	0.3282	2685	X-RAY DIFFRACTION	97
2.2438-2.2773	0.4077	154	0.3103	2667	X-RAY DIFFRACTION	96
2.2773-2.3129	0.3977	131	0.3084	2696	X-RAY DIFFRACTION	97
2.3129-2.3508	0.3944	135	0.3047	2691	X-RAY DIFFRACTION	97
2.3508-2.3913	0.3277	134	0.2906	2735	X-RAY DIFFRACTION	98
2.3913-2.4348	0.3237	138	0.2784	2710	X-RAY DIFFRACTION	98
2.4348-2.4816	0.3714	147	0.2725	2697	X-RAY DIFFRACTION	98
2.4816-2.5322	0.3003	140	0.2563	2733	X-RAY DIFFRACTION	98
2.5322-2.5873	0.3151	150	0.2443	2712	X-RAY DIFFRACTION	98
2.5873-2.6474	0.3083	111	0.2485	2729	X-RAY DIFFRACTION	98
2.6474-2.7136	0.2747	138	0.2359	2759	X-RAY DIFFRACTION	98
2.7136-2.7869	0.3109	143	0.2232	2668	X-RAY DIFFRACTION	98
2.7869-2.8689	0.3027	163	0.2207	2745	X-RAY DIFFRACTION	98
2.8689-2.9614	0.2528	145	0.2188	2755	X-RAY DIFFRACTION	98
2.9614-3.0672	0.3091	149	0.2165	2703	X-RAY DIFFRACTION	98
3.0672-3.1899	0.2904	153	0.2007	2745	X-RAY DIFFRACTION	99
3.1899-3.3349	0.2692	137	0.1964	2741	X-RAY DIFFRACTION	98
3.3349-3.5106	0.2372	153	0.1733	2734	X-RAY DIFFRACTION	99
3.5106-3.7302	0.2109	157	0.1576	2746	X-RAY DIFFRACTION	99
3.7302-4.0177	0.2125	144	0.1418	2758	X-RAY DIFFRACTION	99
4.0177-4.4211	0.1886	145	0.136	2755	X-RAY DIFFRACTION	99
4.4211-5.0587	0.155	140	0.1254	2767	X-RAY DIFFRACTION	99
5.0587-6.3654	0.1883	145	0.158	2783	X-RAY DIFFRACTION	99
6.3654-32.2535	0.1915	166	0.1598	2746	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	1.561	0.2963	0.8785	0.7697	0.4056	1.4605	-0.0375	0.3337	-0.1745	-0.0911	0.0177	-0.3108	0.1775	0.3748	0.0177	0.4681	0.0904	0.0056	0.54	-0.0568	0.4685	27.6129	-17.2978	23.4345
2	0.2228	-0.0392	0.1951	0.9953	0.2078	1.7117	0.1281	0.0403	-0.0653	-0.0319	-0.0399	-0.004	-0.1613	0.0352	-0.0858	0.254	0.0122	-0.0036	0.3219	-0.0055	0.3371	6.8491	-2.1294	26.4146
3	0.4067	0.2743	-0.1543	1.156	0.1817	1.5519	0.0233	0.0666	-0.0542	0.0409	-0.0015	0.0703	-0.0488	0.0029	-0.0268	0.2827	0.0186	0.0024	0.3245	0.0022	0.3292	1.9171	-4.8689	26.495
4	0.3547	0.1478	0.3489	1.008	0.6857	0.9033	0.0251	0.0893	0.1164	-0.1584	0.0082	-0.1349	-0.8203	0.2883	-0.0538	0.6047	-0.1787	0.0861	0.3594	0.0191	0.3863	13.2478	21.8405	23.193
5	0.6974	-0.3751	-0.4192	1.6292	-1.1711	1.9355	0.0686	-0.0395	0.1691	0.3389	-0.0299	0.1931	-0.6158	-0.1857	-0.083	0.6739	0.1034	0.117	0.4079	0.0251	0.3886	-14.1	21.6561	68.1586
6	0.8487	-0.2342	-0.2725	0.307	-0.0512	1.1432	0.0588	-0.0318	-0.0322	-0.0408	0.0191	-0.0384	-0.1686	-0.0658	-0.0443	0.4759	0.0053	0.0298	0.2582	0.0076	0.2896	0.675	10.2783	61.9163
7	1.1023	0.3676	-0.3242	0.5557	-0.1291	1.1709	-0.2229	-0.0979	-0.3614	0.2417	0.0524	-0.0317	0.4374	0.0674	0.1287	0.6152	0.0489	0.0718	0.2935	0.0484	0.3967	1.878	-13.0701	76.5184
8	0.5645	-0.0114	-0.5684	0.8651	-0.202	0.9776	-0.1508	0.0343	-0.0798	0.0168	0.0559	0.0894	0.1285	-0.1322	0.0727	0.4647	-0.0068	0.0747	0.2769	0.02	0.3297	-8.2128	-6.3872	65.8474
9	0.8658	-0.3338	-0.427	0.592	-0.6275	1.5531	-0.0389	0.0155	-0.0605	0.0291	0.0117	-0.0261	-0.2618	0.2309	0.0282	0.4892	-0.1106	-0.0465	0.3913	-0.0275	0.3565	15.8982	6.3495	61.4084
10	0.7752	-0.0926	-0.4735	0.6403	-0.6686	1.1288	-0.1128	-0.1966	0.0511	0.2293	-0.0721	-0.1829	-0.5965	0.6682	0.086	0.6759	-0.2509	-0.0509	0.6193	-0.0164	0.4278	26.8155	14.6496	65.4979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 236 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 237 through 554 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 555 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 185 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 186 through 299 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 300 through 412 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 413 through 554 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 555 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