PDB-6c9x: THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (GH 31) FROM RUMIN...

ID or keywords:

Entry

Database: PDB / ID: 6c9x

Title

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

Components

Glycosyl hydrolase, family 31

Keywords

HYDROLASE / structural genomics / PSI-Biology / alpha-Glucosidase / GH 31 / voglibose / Midwest Center for Structural Genomics / MCSG

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: 1.457 Å

Authors

Tan, K. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

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) 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	Mar 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 21, 2021	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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

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PDBx/mmCIF format	6c9x.cif.gz	570.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6c9x_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6c9x_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6c9x_validation.xml.gz	59.7 KB	Display
Data in CIF	6c9x_validation.cif.gz	92.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9x ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9x	HTTPS FTP

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Related structure data

Related structure data	3n04S S: Starting model for refinement
Similar structure data	1by5-d 6c9z-1 1b0k-d 1qkc-d 4dlg-d 6ca3-1 6ca3-2 1fcp-d 4df4-d 1xvv-1 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: MCSG-APC106690

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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: Glycosyl hydrolase, family 31

B: Glycosyl hydrolase, family 31

hetero molecules

156 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
78.1 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
77.9 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)	64.418, 124.308, 87.741
Angle α, β, γ (deg.)	90.00, 108.50, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Glycosyl hydrolase, family 31 Mass: 77525.578 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 / Cell line (production host): BL21(DE3)magic / Production host: Escherichia coli (E. coli) References: UniProt: A5ZY13, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

#1: Protein

Glycosyl hydrolase, family 31

Mass: 77525.578 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 / Cell line (production host): BL21(DE3)magic / Production host:

Escherichia coli (E. coli)
References: UniProt: A5ZY13, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Non-polymers , 6 types, 1505 molecules

#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 Mass: 267.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₁NO₇ / Comment: inhibitor*YM
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1493 / 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: 2.15 Å³/Da / Density % sol: 42.75 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris, 25% (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 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: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.457→30 Å / Num. obs: 226940 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / B_iso Wilson estimate: 13.56 Å² / R_merge(I) obs: 0.075 / R_pim(I) all: 0.041 / R_rim(I) all: 0.086 / Χ²: 1.046 / Net I/σ(I): 20.8
Reflection shell	Resolution: 1.46→1.49 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.625 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11315 / CC_1/2: 0.731 / R_pim(I) all: 0.348 / R_rim(I) all: 0.718 / Χ²: 0.659 / % possible all: 100

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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: 3N04

3n04

Resolution: 1.457→29.886 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.55

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1623	11379	5.02 %	Random
R_work	0.1418	-	-	-
obs	0.1428	226890	99.7 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.457→29.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10820	0	60	1493	12373

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	11270
X-RAY DIFFRACTION	f_angle_d	1.151	15231
X-RAY DIFFRACTION	f_dihedral_angle_d	13.418	4205
X-RAY DIFFRACTION	f_chiral_restr	0.083	1538
X-RAY DIFFRACTION	f_plane_restr	0.006	1997

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 (%)
1.457-1.4736	0.2514	326	0.2252	6567	X-RAY DIFFRACTION	91
1.4736-1.4909	0.2268	397	0.2103	7214	X-RAY DIFFRACTION	100
1.4909-1.5091	0.2385	369	0.2076	7169	X-RAY DIFFRACTION	100
1.5091-1.5282	0.2258	393	0.1967	7210	X-RAY DIFFRACTION	100
1.5282-1.5483	0.2352	382	0.1874	7110	X-RAY DIFFRACTION	100
1.5483-1.5695	0.2002	379	0.1778	7301	X-RAY DIFFRACTION	100
1.5695-1.5919	0.1927	355	0.1641	7111	X-RAY DIFFRACTION	100
1.5919-1.6157	0.1847	405	0.1609	7212	X-RAY DIFFRACTION	100
1.6157-1.6409	0.1876	362	0.1545	7178	X-RAY DIFFRACTION	100
1.6409-1.6678	0.1984	386	0.1484	7142	X-RAY DIFFRACTION	100
1.6678-1.6966	0.1785	389	0.1496	7218	X-RAY DIFFRACTION	100
1.6966-1.7274	0.18	402	0.1419	7171	X-RAY DIFFRACTION	100
1.7274-1.7606	0.1685	355	0.1418	7200	X-RAY DIFFRACTION	100
1.7606-1.7966	0.1804	383	0.1446	7200	X-RAY DIFFRACTION	100
1.7966-1.8356	0.177	416	0.1396	7201	X-RAY DIFFRACTION	100
1.8356-1.8783	0.1658	401	0.1395	7125	X-RAY DIFFRACTION	100
1.8783-1.9253	0.1689	334	0.1412	7252	X-RAY DIFFRACTION	100
1.9253-1.9773	0.1747	351	0.1418	7245	X-RAY DIFFRACTION	100
1.9773-2.0355	0.1676	379	0.1401	7202	X-RAY DIFFRACTION	100
2.0355-2.1012	0.145	377	0.1348	7171	X-RAY DIFFRACTION	100
2.1012-2.1763	0.1582	355	0.1335	7238	X-RAY DIFFRACTION	100
2.1763-2.2634	0.1509	401	0.139	7206	X-RAY DIFFRACTION	100
2.2634-2.3664	0.1609	350	0.1412	7239	X-RAY DIFFRACTION	100
2.3664-2.4911	0.1587	391	0.1409	7205	X-RAY DIFFRACTION	100
2.4911-2.647	0.1691	421	0.1445	7166	X-RAY DIFFRACTION	100
2.647-2.8513	0.1712	362	0.1467	7249	X-RAY DIFFRACTION	100
2.8513-3.1379	0.1537	396	0.1455	7203	X-RAY DIFFRACTION	100
3.1379-3.5913	0.1418	389	0.1323	7232	X-RAY DIFFRACTION	100
3.5913-4.5222	0.1271	378	0.116	7266	X-RAY DIFFRACTION	100
4.5222-29.892	0.1486	395	0.1327	7308	X-RAY DIFFRACTION	100

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	2.57	0.5515	1.4165	1.4109	0.8446	1.7913	0.0706	0.2298	-0.1576	-0.057	0.0543	-0.1789	0.0656	0.1686	-0.116	0.1248	0.0193	0.0183	0.1343	-0.0238	0.1499	41.5152	-19.0615	-18.3304
2	0.4668	-0.1456	0.0578	0.5177	-0.0191	0.3113	-0.0058	-0.0058	-0.004	0.0088	0.0036	0.0482	-0.0135	-0.0333	0.0008	0.0908	-0.0082	0.0038	0.0824	-0.0063	0.0819	20.4482	-3.8334	-15.3247
3	1.4411	0.0484	-0.5863	2.7941	0.7096	1.5636	-0.0632	0.0462	-0.0455	0.0528	-0.0055	0.1482	0.1002	-0.0878	0.0639	0.1189	-0.0305	0.0008	0.1099	-0.0021	0.1166	5.6942	-23.4242	-21.6803
4	0.6885	0.2747	-0.3151	0.9001	-0.0703	1.6288	-0.032	-0.089	-0.0604	0.155	-0.0797	0.0716	0.2417	-0.0451	0.1078	0.144	-0.025	0.026	0.109	-0.0269	0.1216	6.9798	-18.9788	-10.0641
5	1.3887	-0.4312	0.5186	2.4818	-0.7933	1.4844	0.0008	-0.0217	-0.0785	-0.0125	-0.0068	-0.0155	0.164	0.0348	0.0306	0.0758	-0.0063	0.0013	0.0628	-0.0209	0.0726	17.7964	-20.953	-19.5866
6	0.2323	0.0127	0.0419	0.4485	0.1977	0.5291	-0.0151	-0.0032	-0.0115	0.0059	-0.0007	0.0402	-0.0308	-0.0171	0.0168	0.1262	-0.0044	-0.0036	0.1122	0.0066	0.1034	21.3306	6.4739	-14.2482
7	0.5216	0.1558	0.3157	0.6182	0.2944	1.1295	-0.063	0.0627	0.0675	-0.1363	0.0299	0.031	-0.1856	0.0715	0.0324	0.1472	-0.0188	-0.0024	0.0896	0.0136	0.1086	27.253	19.859	-18.2689
8	0.8567	-0.2072	-0.2365	0.877	0.0573	1.0384	-0.0033	0.022	0.0439	0.0161	0.0324	0.0424	-0.0568	-0.0513	-0.0233	0.1036	0.0061	0.001	0.1013	0.0116	0.1002	6.0407	15.2946	19.8684
9	0.5835	0.2355	-0.2674	0.2673	-0.1161	0.3209	-0.0461	-0.0326	-0.1135	-0.0033	-0.0016	-0.0427	0.07	0.007	0.0399	0.1047	0.005	-0.003	0.0938	0.0023	0.0915	21.2022	-3.5533	24.4838
10	0.5913	0.716	-0.2007	2.0856	-0.6642	1.0068	0.1074	-0.2377	-0.0332	0.1927	-0.1262	-0.1558	-0.0899	0.1614	0.0237	0.1284	-0.0239	-0.0414	0.2114	0.0031	0.1191	39.6385	12.3894	36.1027

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 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 282 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 283 through 349 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 350 through 393 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 394 through 554 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 555 through 663 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 151 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 152 through 608 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 609 through 663 )

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