PDB-4yyf: The crystal structure of a glycosyl hydrolase of GH3 family membe...

ID or keywords:

Entry

Database: PDB / ID: 4yyf

Title

The crystal structure of a glycosyl hydrolase of GH3 family member from [Mycobacterium smegmatis str. MC2 155

Components

Beta-N-acetylhexosaminidase

Hexosaminidase

Keywords

HYDROLASE /

structural genomics / PSI-Biology /

protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Function and homology information

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

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.92 Å

Authors

Tan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of a glycosyl hydrolase of GH3 family member from [Mycobacterium smegmatis str. MC2 155
Authors: Tan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.

History

Deposition	Mar 23, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yyf.cif.gz	367.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4yyf.ent.gz	314.1 KB	Display	PDB format
PDBx/mmJSON format	4yyf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yy/4yyf ftp://data.pdbj.org/pub/pdb/validation_reports/yy/4yyf	HTTPS FTP

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Related structure data

Similar structure data	5gp1-2 5ec8-1 5wz2-2 5wz2-1 5afd-d 5ehg-1 6gfv-1 5wz1-2 5ehg-2 4ee7-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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-APC100128

Similar structure data

Other databases

TargetTrack: MCSG-APC100128

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-N-acetylhexosaminidase

B: Beta-N-acetylhexosaminidase

C: Beta-N-acetylhexosaminidase

hetero molecules

113 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-N-acetylhexosaminidase

hetero molecules

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

2

B: Beta-N-acetylhexosaminidase

hetero molecules

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

3

C: Beta-N-acetylhexosaminidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	103.067, 130.941, 85.986
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 3 molecules ABC

#1: Protein	Beta-N-acetylhexosaminidase / Hexosaminidase Mass: 37455.484 Da / Num. of mol.: 3 / Mutation: A291V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0361, MSMEI_0354, LJ00_01805 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0QPD6, beta-N-acetylhexosaminidase

#1: Protein

Beta-N-acetylhexosaminidase /

Hexosaminidase

Mass: 37455.484 Da / Num. of mol.: 3 / Mutation: A291V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0361, MSMEI_0354, LJ00_01805 / Plasmid: pMCSG68 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0QPD6,

beta-N-acetylhexosaminidase

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Non-polymers , 5 types, 564 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#5: 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
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.9 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8M Sodium Acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2015
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.92→36.5 Å / Num. obs: 89349 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / R_merge(I) obs: 0.093 / Net I/σ(I): 23.3
Reflection shell	Resolution: 1.92→1.95 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.771 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
SBC-Collect		data collection
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.92→36.41 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2101	4376	4.94 %	Random selection
R_work	0.179	-	-	-
obs	0.1805	88553	99.05 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.92→36.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7044	0	36	553	7633

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7202
X-RAY DIFFRACTION	f_angle_d	1.11	9816
X-RAY DIFFRACTION	f_dihedral_angle_d	12.092	2548
X-RAY DIFFRACTION	f_chiral_restr	0.075	1153
X-RAY DIFFRACTION	f_plane_restr	0.005	1314

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 (%)
1.9199-1.9417	0.3026	144	0.2571	2352	X-RAY DIFFRACTION	85
1.9417-1.9646	0.2767	158	0.2508	2571	X-RAY DIFFRACTION	93
1.9646-1.9885	0.2695	153	0.2356	2747	X-RAY DIFFRACTION	98
1.9885-2.0137	0.2447	146	0.2246	2758	X-RAY DIFFRACTION	99
2.0137-2.0402	0.2526	166	0.2212	2771	X-RAY DIFFRACTION	100
2.0402-2.0681	0.2671	129	0.2228	2804	X-RAY DIFFRACTION	100
2.0681-2.0977	0.2499	125	0.2197	2834	X-RAY DIFFRACTION	100
2.0977-2.129	0.2116	137	0.2114	2785	X-RAY DIFFRACTION	100
2.129-2.1623	0.2484	150	0.1958	2819	X-RAY DIFFRACTION	100
2.1623-2.1977	0.2204	143	0.1921	2808	X-RAY DIFFRACTION	100
2.1977-2.2356	0.2363	150	0.1974	2790	X-RAY DIFFRACTION	100
2.2356-2.2762	0.2509	155	0.19	2803	X-RAY DIFFRACTION	100
2.2762-2.32	0.2183	128	0.1912	2802	X-RAY DIFFRACTION	100
2.32-2.3674	0.2387	131	0.1813	2803	X-RAY DIFFRACTION	100
2.3674-2.4188	0.2177	163	0.1828	2812	X-RAY DIFFRACTION	100
2.4188-2.4751	0.2187	156	0.1742	2803	X-RAY DIFFRACTION	100
2.4751-2.537	0.1982	136	0.1803	2834	X-RAY DIFFRACTION	100
2.537-2.6055	0.252	147	0.1878	2825	X-RAY DIFFRACTION	100
2.6055-2.6822	0.2177	142	0.1791	2812	X-RAY DIFFRACTION	100
2.6822-2.7687	0.1892	132	0.1792	2817	X-RAY DIFFRACTION	100
2.7687-2.8676	0.2316	183	0.1767	2820	X-RAY DIFFRACTION	100
2.8676-2.9824	0.1872	139	0.1819	2840	X-RAY DIFFRACTION	100
2.9824-3.1181	0.223	152	0.1818	2822	X-RAY DIFFRACTION	100
3.1181-3.2824	0.1961	150	0.17	2851	X-RAY DIFFRACTION	100
3.2824-3.4879	0.1934	134	0.1532	2850	X-RAY DIFFRACTION	100
3.4879-3.7569	0.1561	141	0.143	2872	X-RAY DIFFRACTION	100
3.7569-4.1345	0.1554	140	0.1426	2891	X-RAY DIFFRACTION	100
4.1345-4.7317	0.178	129	0.14	2903	X-RAY DIFFRACTION	100
4.7317-5.9572	0.161	146	0.1718	2935	X-RAY DIFFRACTION	100
5.9572-36.417	0.2406	171	0.2053	3043	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	3.3471	0.5573	0.8465	3.2849	1.0549	1.8371	0.0412	-0.1471	-0.0868	0.0992	-0.06	0.2379	0.0501	-0.1758	0.0389	0.0945	0.0002	-0.0042	0.0995	0.0062	0.1316	88.6967	50.9538	78.4874
2	1.7443	-0.5666	-1.3784	1.3444	0.5151	3.1458	-0.0619	-0.0142	0.1283	-0.0655	0.0612	0.0938	-0.1372	-0.0094	-0.0229	0.1327	-0.0134	-0.0155	0.1287	-0.0031	0.185	101.2467	53.4624	78.8493
3	1.3275	-0.7944	0.7437	1.6123	0.1327	0.7253	0.0004	0.1448	0.048	-0.389	0.1582	-0.207	-0.1595	0.4011	-0.1937	0.1729	-0.0601	0.0558	0.2394	0.0108	0.1982	118.4864	47.486	67.6976
4	1.0867	0.176	0.3381	1.0192	0.3314	1.7745	-0.0889	0.1606	-0.0723	-0.2423	0.0532	-0.1239	0.0511	0.118	0.036	0.1437	-0.024	0.0434	0.1263	0.0014	0.1209	107.9096	40.1635	64.719
5	0.4966	-0.1669	-0.4178	1.595	0.1376	0.9725	-0.0405	0.2097	-0.054	-0.3444	-0.0602	0.2381	-0.048	-0.1524	0.0907	0.1746	-0.0389	-0.0508	0.1632	-0.0161	0.148	89.7954	42.7578	63.5545
6	3.4737	0.4527	2.194	3.1116	-0.2467	3.5795	-0.0888	-0.0867	0.0841	-0.0019	0.0097	0.2389	0.0904	-0.2025	0.0959	0.1275	-0.0282	0.0351	0.1114	-0.0023	0.1842	85.864	38.1417	77.8177
7	4.2109	-0.1145	-1.5404	0.7352	-0.8725	3.4002	-0.0883	0.2198	0.4012	-0.1475	0.1921	0.1287	-0.2434	-0.1151	-0.1234	0.1849	-0.0677	-0.0648	0.1771	0.0572	0.1641	63.3805	24.2693	67.4266
8	1.6798	-0.6303	0.2345	2.758	-0.6597	1.9388	-0.1651	0.3018	0.169	-0.2641	0.1699	0.0207	-0.0825	-0.0885	0.0091	0.1947	-0.1054	-0.0305	0.2369	0.0397	0.1906	76.0429	24.741	65.3088
9	1.1075	0.7218	-0.5337	1.6539	-0.5574	0.6892	-0.0789	-0.007	-0.1251	-0.1133	0.0295	-0.2212	0.0516	0.0931	0.0498	0.112	-0.0182	0.0034	0.1486	-0.0047	0.1456	82.2353	10.683	78.3451
10	1.1308	0.0474	0.0855	1.2181	-0.3548	1.5317	-0.1127	0.1422	-0.0976	-0.1592	0.1082	0.0608	0.0917	-0.0909	0.0007	0.0992	-0.0417	0.0069	0.1283	0.0091	0.107	65.3027	9.2626	75.8182
11	2.5803	-0.0731	0.3575	0.6211	0.4241	3.1137	-0.1154	0.0882	0.1741	-0.1433	0.0785	0.1927	-0.195	-0.1657	0.0149	0.131	-0.0064	-0.027	0.1177	0.0422	0.1489	56.9372	20.2822	76.2263
12	3.4284	-0.594	-0.8315	4.1226	1.2826	1.5977	0.0166	0.7091	0.0199	0.2748	-0.0844	-0.4677	-0.0834	0.5297	0.0658	0.507	-0.0646	-0.0498	0.842	0.0014	0.4874	95.9406	14.1924	45.7269
13	1.4752	0.0899	-0.0776	1.2162	0.0192	1.4641	0.2158	0.1032	-0.2612	-0.0229	-0.0136	-0.4206	0.3035	0.7003	-0.1964	0.6008	0.0701	-0.1121	0.7299	-0.0652	0.5164	86.4134	-3.5421	41.8856
14	2.6285	0.9229	-1.6786	2.877	-0.4259	1.2657	0.0139	-0.5955	-0.4418	0.2877	-0.0943	-0.6077	0.2562	0.4231	0.0561	0.6781	0.0707	-0.2018	0.6508	0.0103	0.4607	83.9429	-8.145	49.0236
15	0.9983	0.0046	-0.1506	0.8373	0.1431	0.8725	0.0455	-0.0176	-0.1547	0.0476	-0.0321	0.0169	0.2607	0.0354	-0.0021	0.5968	-0.0486	-0.0545	0.5328	-0.012	0.3485	69.7538	-0.2955	43.5498
16	2.789	-0.7805	1.1875	0.6974	0.4747	1.8648	0.2028	-0.3122	-0.1347	-0.0337	-0.043	0.0628	0.0917	0.1337	-0.1934	0.4816	0.0132	-0.0488	0.5744	0.0581	0.3384	71.449	10.0657	43.2055
17	1.0545	0.0472	0.5096	0.6484	-0.1885	0.7664	-0.0346	0.1829	0.1361	-0.0996	-0.0012	-0.0573	-0.1159	0.174	0.042	0.5565	-0.0342	-0.0258	0.6094	-0.0212	0.349	80.0403	16.4058	41.6049
18	0.8293	-1.0335	-0.6564	5.0471	-0.9907	1.4974	-0.0942	-0.0575	0.2952	0.5848	-0.023	-0.6658	-0.3641	0.7047	0.1365	0.6817	-0.173	-0.1724	0.728	-0.0238	0.4065	87.4816	16.9345	54.2088

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 56 through 98 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 99 through 135 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 136 through 153 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 154 through 263 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 264 through 362 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 363 through 386 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 56 through 98 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 99 through 135 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 136 through 283 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 284 through 348 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 349 through 385 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 56 through 88 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 89 through 153 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 154 through 181 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 182 through 263 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 264 through 283 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 284 through 362 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 363 through 386 )

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