PDB-4zmh: Crystal structure of a five-domain GH115 alpha-Glucuronidase from...

ID or keywords:

Entry

Database: PDB / ID: 4zmh

Title

Crystal structure of a five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T

Components

Uncharacterized protein

Keywords

HYDROLASE /

glycosyl hydrolase

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Saccharophagus degradans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.93 Å

Authors

Nocek, B. / Cui, H. / Wang, W. / Savchenko, A.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Biochemical and Structural Characterization of a Five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T.
Authors: Wang, W. / Yan, R. / Nocek, B.P. / Vuong, T.V. / Di Leo, R. / Xu, X. / Cui, H. / Gatenholm, P. / Toriz, G. / Tenkanen, M. / Savchenko, A. / Master, E.R.

History

Deposition	May 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 11, 2016	Group: Database references
Revision 1.2	May 18, 2016	Group: Structure summary
Revision 1.3	Jul 13, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zmh.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4zmh.ent.gz	968 KB	Display	PDB format
PDBx/mmJSON format	4zmh.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/zm/4zmh ftp://data.pdbj.org/pub/pdb/validation_reports/zm/4zmh	HTTPS FTP

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Related structure data

Similar structure data	9655 1m56-d 1m57-d 2hau-d 5weh-d 0940 4g7n-2 2hav-d 4dur-d 6mdz-d Search similar-shape structures by Omokage search (details) 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	#141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	116.442, 124.294, 180.027
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Uncharacterized protein Mass: 107154.203 Da / Num. of mol.: 2 / Fragment: UNP residues 37-975 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharophagus degradans (bacteria) / Strain: 2-40 / ATCC 43961 / DSM 17024 / Gene: Sde_1755 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21JW4

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Non-polymers , 5 types, 2190 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2181 / 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: 3.07 Å³/Da / Density % sol: 59.98 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium dihydrogen phosphate, 20%PEG3350, 0.1M citric acid

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.93→40 Å / Num. obs: 188525 / % possible obs: 97.7 % / Redundancy: 4.9 % / Net I/σ(I): 19

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Processing

Software

Name	Version	Classification
PHENIX	dev_1834	refinement
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.93→38.148 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1701	9196	5.01 %
R_work	0.1383	-	-
obs	0.1399	183413	93.74 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.93→38.148 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14860	0	38	2181	17079

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	15460
X-RAY DIFFRACTION	f_angle_d	1.171	21083
X-RAY DIFFRACTION	f_dihedral_angle_d	14.153	5630
X-RAY DIFFRACTION	f_chiral_restr	0.051	2244
X-RAY DIFFRACTION	f_plane_restr	0.006	2743

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 (%)
1.93-1.9523	0.2412	144	0.2245	2541	X-RAY DIFFRACTION	41
1.9523-1.9753	0.2419	239	0.2179	4793	X-RAY DIFFRACTION	78
1.9753-1.9994	0.2465	320	0.2028	5078	X-RAY DIFFRACTION	84
1.9994-2.0247	0.2531	283	0.1985	5388	X-RAY DIFFRACTION	88
2.0247-2.0513	0.2165	295	0.1925	5575	X-RAY DIFFRACTION	91
2.0513-2.0794	0.2123	326	0.1827	5680	X-RAY DIFFRACTION	92
2.0794-2.1092	0.21	300	0.1694	5719	X-RAY DIFFRACTION	94
2.1092-2.1406	0.2047	306	0.1675	5854	X-RAY DIFFRACTION	95
2.1406-2.1741	0.1932	314	0.157	5893	X-RAY DIFFRACTION	96
2.1741-2.2097	0.1774	326	0.1561	5952	X-RAY DIFFRACTION	97
2.2097-2.2478	0.1843	283	0.1518	6027	X-RAY DIFFRACTION	97
2.2478-2.2887	0.1783	307	0.1447	5989	X-RAY DIFFRACTION	97
2.2887-2.3327	0.1771	292	0.141	6059	X-RAY DIFFRACTION	98
2.3327-2.3803	0.1736	343	0.1366	6009	X-RAY DIFFRACTION	98
2.3803-2.4321	0.1618	324	0.1369	6044	X-RAY DIFFRACTION	98
2.4321-2.4886	0.1776	331	0.135	6037	X-RAY DIFFRACTION	98
2.4886-2.5508	0.161	297	0.1333	6062	X-RAY DIFFRACTION	98
2.5508-2.6198	0.1842	310	0.1349	6090	X-RAY DIFFRACTION	98
2.6198-2.6969	0.1681	360	0.1367	6054	X-RAY DIFFRACTION	98
2.6969-2.7839	0.1898	354	0.1356	6066	X-RAY DIFFRACTION	98
2.7839-2.8834	0.1675	324	0.1341	6089	X-RAY DIFFRACTION	99
2.8834-2.9988	0.1733	312	0.1362	6092	X-RAY DIFFRACTION	98
2.9988-3.1352	0.1737	295	0.1327	6139	X-RAY DIFFRACTION	99
3.1352-3.3004	0.1672	313	0.1298	6148	X-RAY DIFFRACTION	98
3.3004-3.507	0.1481	327	0.1271	6094	X-RAY DIFFRACTION	98
3.507-3.7776	0.1586	296	0.1249	6184	X-RAY DIFFRACTION	98
3.7776-4.1573	0.1401	315	0.1111	6147	X-RAY DIFFRACTION	98
4.1573-4.7579	0.1274	326	0.1029	6151	X-RAY DIFFRACTION	98
4.7579-5.9907	0.1476	311	0.1193	6150	X-RAY DIFFRACTION	97
5.9907-38.1551	0.1684	323	0.1613	6113	X-RAY DIFFRACTION	93

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	0.5564	0.0968	0.0077	0.5471	0.111	0.51	-0.0906	-0.1402	0.3841	0.0693	-0.0522	0.0935	-0.2922	-0.1051	0.0749	0.2596	0.0683	-0.099	0.1818	-0.1173	0.3663	32.5544	115.8392	106.9936
2	1.4333	-0.5851	-0.2325	0.4774	-0.1884	1.2574	-0.0056	0.295	0.2874	-0.2165	-0.1049	-0.1702	-0.1556	0.1988	0.087	0.2635	-0.0389	-0.0306	0.2318	0.1169	0.3163	50.9935	109.7472	77.3618
3	0.4874	0.1109	0.1499	0.5864	0.0966	0.3461	-0.0447	-0.0661	0.1341	0.0446	-0.013	0.0458	-0.035	-0.0321	0.0549	0.097	0.0165	-0.0195	0.129	-0.0278	0.1042	31.2533	85.5982	97.0663
4	0.7336	0.3132	0.1709	1.0249	0.0652	0.5777	0.1192	-0.233	-0.1745	0.2459	-0.0968	-0.0564	0.1939	-0.1256	-0.0274	0.1932	0.0004	0.0146	0.1932	0.0265	0.1029	31.6534	57.2185	107.0397
5	0.8726	-0.1975	0.3409	1.3706	-0.4002	0.7691	-0.0062	-0.0652	-0.0195	0.0539	-0.0185	-0.1799	0.0483	0.0571	0.0261	0.1145	0.0243	-0.0114	0.1368	-0.0101	0.104	50.7089	70.6999	104.2511
6	0.6284	-0.054	0.0239	0.9464	0.4119	0.8456	-0.0627	0.2028	-0.1746	-0.3535	-0.0017	0.1938	0.0192	-0.1864	0.0537	0.2493	-0.0835	-0.0289	0.2606	-0.0546	0.1851	-0.8399	12.499	45.8535
7	0.9174	0.0113	-0.1482	1.2015	0.2178	0.4915	-0.0401	-0.0884	-0.0523	0.0809	0.0412	-0.0308	0.0465	0.0078	-0.0017	0.1317	-0.031	-0.0075	0.1419	-0.0061	0.1104	8.3727	20.1204	68.5505
8	1.531	0.2319	-0.1318	0.7326	-0.3786	1.3201	0.0969	-0.3192	-0.2675	0.4276	0.0237	-0.5643	0.117	0.3057	-0.1211	0.2752	0.0281	-0.1192	0.2336	-0.0147	0.3617	24.9764	10.3474	77.1878
9	0.2251	0.3816	0.1609	0.9543	0.3013	0.2762	-0.0714	0.074	-0.0054	-0.2286	0.0875	-0.0514	-0.0914	0.036	-0.0126	0.1655	-0.0417	0.0124	0.1607	-0.0196	0.1109	16.7607	45.7316	62.9925
10	0.2571	0.0794	0.06	0.6117	0.1153	0.7189	-0.2423	0.2722	0.057	-0.5339	0.0846	-0.2358	-0.3367	-0.0036	-0.0838	0.5146	-0.2222	0.1274	0.3218	0.0113	0.1983	33.1528	76.2985	56.0237
11	1.7367	-1.1177	-0.3209	1.0534	0.4954	0.4242	-0.0054	0.2415	-0.1587	-0.2654	0.0365	-0.2951	-0.0069	0.1921	0.0555	0.3347	-0.1227	0.2322	0.3632	-0.1586	0.3697	37.525	35.4747	48.3767
12	0.8876	0.2632	-0.3882	0.4851	-0.0356	0.6339	0.0348	0.0931	-0.1141	-0.3105	0.1821	-0.6078	-0.1823	0.4024	0.0414	0.1996	-0.2008	0.2328	0.3968	-0.2117	0.4686	42.2902	44.3965	56.6221

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 41 through 290 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 291 through 364 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 365 through 703 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 704 through 844 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 845 through 974 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 41 through 184 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 185 through 305 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 306 through 402 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 403 through 703 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 704 through 808 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 809 through 849 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 850 through 975 )

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