PDB-5ohz: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat...

ID or keywords:

Entry

Database: PDB / ID: 5ohz

Title

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) - SeMet derivative

Components

Hydrolase

Keywords

HYDROLASE /

Mycobacterium

Function / homology

Function and homology information

glucosylglycerate hydrolase / glucosylglycerate hydrolase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process
Similarity search - Function

Biological species

Mycobacterium hassiacum DSM 44199 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.036 Å

Authors

Cereija, T.B. / Macedo-Ribeiro, S. / Pereira, P.J.B.

Funding support

Portugal, 2items

Citation

Journal: Iucrj / Year: 2019
Title: The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation.
Authors: Cereija, T.B. / Alarico, S. / Lourenco, E.C. / Manso, J.A. / Ventura, M.R. / Empadinhas, N. / Macedo-Ribeiro, S. / Pereira, P.J.B.

History

Deposition	Jul 18, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2019	Group: Data collection / Database references / Structure summary Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info / struct Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct.title
Revision 1.2	Jul 31, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Aug 28, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ohz.cif.gz	751.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ohz.ent.gz	644.1 KB	Display	PDB format
PDBx/mmJSON format	5ohz.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/oh/5ohz ftp://data.pdbj.org/pub/pdb/validation_reports/oh/5ohz	HTTPS FTP

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Related structure data

Related structure data	5ohcC 5oi0C 5oi1C 5oieC 5oivC 5oiwC 5oj4C 5ojuC 5ojvC 5ontC 5onzC 5oo2C 6q5tC C: citing same article (ref.)
Similar structure data	5oi1-1 5oie-1 5onz-1 5ont-1 6g3n-1 5oj4-1 5oiw-1 5oi0-1 5ojv-1 5oiv-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/465 / Data set type: diffraction image data
Experimental dataset #2	Data reference: 10.15785/SBGRID/466 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (2)

Deposited unit

A: Hydrolase

B: Hydrolase

C: Hydrolase

D: Hydrolase

hetero molecules

208 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS, gel filtration

Unit cell

Length a, b, c (Å)	90.750, 86.101, 159.720
Angle α, β, γ (deg.)	90.00, 93.03, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hydrolase / Mass: 51411.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium hassiacum DSM 44199 (bacteria) Gene: C731_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDL0
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Formula: C₃H₈O₃
#3: Chemical	ChemComp-SER / SERINE / Serine Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1289 / 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: 3.07 Å³/Da / Density % sol: 59.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Tris-Bicine pH 8.5, amino acids, PEG 4000, glycerol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.97909, 0.97924

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2015

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97909	1
2	0.97924	1

Reflection

Resolution: 2.036→57.421 Å / Num. obs: 255146 / % possible obs: 96.5 % / Redundancy: 2.8 % / CC_1/2: 0.99 / R_merge(I) obs: 0.105 / R_pim(I) all: 0.072 / R_rim(I) all: 0.128 / Net I/σ(I): 7.6

Reflection shell

Resolution: 2.04→2.07 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.637 / Mean I/σ(I) obs: 1.6 / CC_1/2: 0.659 / R_pim(I) all: 0.438 / R_rim(I) all: 0.776 / % possible all: 82.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XDS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.036→57.421 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.44

	R_factor	Num. reflection	% reflection
R_free	0.2446	12657	4.96 %
R_work	0.1989	-	-
obs	0.2012	255146	82.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.036→57.421 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14266	0	124	1289	15679

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	15101
X-RAY DIFFRACTION	f_angle_d	1.099	20578
X-RAY DIFFRACTION	f_dihedral_angle_d	18.866	8872
X-RAY DIFFRACTION	f_chiral_restr	0.058	2117
X-RAY DIFFRACTION	f_plane_restr	0.007	2697

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 (%)
2.0362-2.0593	0.3606	321	0.3173	5895	X-RAY DIFFRACTION	60
2.0593-2.0836	0.3096	441	0.2906	8205	X-RAY DIFFRACTION	83
2.0836-2.109	0.3297	425	0.2801	8210	X-RAY DIFFRACTION	83
2.109-2.1357	0.326	469	0.2796	8040	X-RAY DIFFRACTION	83
2.1357-2.1638	0.3205	460	0.2756	8227	X-RAY DIFFRACTION	83
2.1638-2.1934	0.321	433	0.271	8068	X-RAY DIFFRACTION	83
2.1934-2.2248	0.3261	401	0.2698	8172	X-RAY DIFFRACTION	83
2.2248-2.258	0.3133	361	0.2684	8271	X-RAY DIFFRACTION	83
2.258-2.2932	0.3339	384	0.2615	8126	X-RAY DIFFRACTION	83
2.2932-2.3308	0.3301	369	0.2375	8247	X-RAY DIFFRACTION	83
2.3308-2.371	0.2915	424	0.241	8157	X-RAY DIFFRACTION	83
2.371-2.4142	0.3079	441	0.24	7895	X-RAY DIFFRACTION	81
2.4142-2.4606	0.2831	447	0.237	7547	X-RAY DIFFRACTION	77
2.4606-2.5108	0.2864	469	0.2286	8098	X-RAY DIFFRACTION	84
2.5108-2.5654	0.2823	419	0.2265	8218	X-RAY DIFFRACTION	84
2.5654-2.6251	0.3037	436	0.2193	8291	X-RAY DIFFRACTION	84
2.6251-2.6907	0.2369	446	0.2032	8141	X-RAY DIFFRACTION	83
2.6907-2.7635	0.2688	373	0.2064	8238	X-RAY DIFFRACTION	83
2.7635-2.8448	0.2627	350	0.213	8273	X-RAY DIFFRACTION	84
2.8448-2.9366	0.2625	452	0.1988	8087	X-RAY DIFFRACTION	83
2.9366-3.0416	0.2448	484	0.2053	8073	X-RAY DIFFRACTION	83
3.0416-3.1633	0.2534	430	0.2022	7713	X-RAY DIFFRACTION	79
3.1633-3.3073	0.2271	413	0.1806	7974	X-RAY DIFFRACTION	81
3.3073-3.4816	0.2363	425	0.1802	8293	X-RAY DIFFRACTION	84
3.4816-3.6997	0.2165	374	0.1731	8255	X-RAY DIFFRACTION	84
3.6997-3.9853	0.2059	375	0.1617	8295	X-RAY DIFFRACTION	84
3.9853-4.3863	0.1784	492	0.1506	8139	X-RAY DIFFRACTION	84
4.3863-5.0207	0.179	433	0.1508	8186	X-RAY DIFFRACTION	83
5.0207-6.3242	0.2146	471	0.1705	8670	X-RAY DIFFRACTION	89
6.3242-57.4441	0.2131	439	0.1807	8485	X-RAY DIFFRACTION	87

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	3.4795	0.6463	2.9114	0.9529	-1.0802	5.714	-0.0752	0.0419	-0.005	-0.143	0.0341	-0.083	-0.0259	0.0709	0.0459	0.1509	0.0121	0.053	0.1207	-0.0204	0.148	45.6542	22.3812	129.2835
2	5.844	0.8273	0.22	8.427	0.0351	3.75	-0.061	0.1121	0.0469	-0.2887	0.0068	-0.4828	-0.0728	0.5151	0.0744	0.1601	0.0103	-0.0008	0.2834	-0.0267	0.1419	59.0799	22.3946	144.3817
3	1.1869	-0.1136	-0.0261	0.9282	-0.1283	0.8894	-0.0022	-0.2468	0.1041	0.1145	-0.0171	0.0107	-0.1053	-0.0032	0.0159	0.1972	0.0056	-0.0001	0.1886	-0.0318	0.1534	39.8404	25.8283	146.7466
4	4.0916	0.0131	-3.08	0.4055	-0.9978	4.8717	-0.0435	-0.0348	-0.0683	0.0892	-0.0487	-0.0781	0.1121	0.1563	0.0883	0.1919	-0.0171	-0.0279	0.1307	-0.01	0.1306	46.9504	22.054	110.2777
5	5.4228	0.2892	-0.4606	6.9388	0.4513	1.8798	0.0737	-0.1448	-0.1344	0.1997	-0.0914	-0.6553	0.1272	0.3677	0.0369	0.1622	0.0156	-0.0069	0.3264	-0.0087	0.1835	61.7011	21.9052	97.1375
6	2.6689	0.3406	-0.8928	1.7151	-0.1429	3.1698	0.1033	0.0436	0.4671	0.1101	-0.0225	0.025	-0.2843	-0.0348	-0.109	0.2282	-0.0152	-0.0098	0.1455	0.035	0.2255	44.6338	36.1124	100.6799
7	0.9596	0.126	-0.1241	1.0944	-0.0215	1.1469	-0.029	0.2832	-0.1412	-0.1624	0.014	-0.0216	0.2321	-0.0096	0.0147	0.2465	-0.0105	0.0092	0.2239	-0.0444	0.1676	41.9788	15.2789	91.3956
8	4.2483	2.0306	-1.0154	1.6188	-1.8042	3.001	-0.0954	0.3635	0.0661	-0.0951	0.2169	0.1869	0.175	-0.491	-0.1101	0.186	0.0076	-0.0204	0.2875	0.0642	0.2236	1.7438	16.4848	125.1398
9	4.3264	1.8629	-0.4946	3.3253	0.1118	0.7933	-0.0776	0.2026	0.079	-0.1624	0.1652	0.4934	0.0067	-0.3693	-0.0769	0.2118	0.0227	-0.0183	0.3932	0.104	0.2766	-7.4263	12.5889	136.6563
10	1.7	0.1682	0.0449	1.4384	-0.167	1.4593	-0.0081	-0.1626	-0.2466	0.0473	0.105	0.2441	0.2225	-0.4097	-0.0645	0.2126	-0.0358	0.0078	0.3566	0.1042	0.3106	-0.9168	3.0284	143.204
11	1.5519	0.1989	0.447	1.2511	-0.0743	2.3929	0.0384	0.0887	-0.2061	-0.1455	0.0221	-0.1166	0.304	-0.01	-0.0646	0.2297	0.0032	0.0226	0.2214	0.0182	0.2861	15.0975	2.43	130.627
12	5.4258	-3.2689	1.3073	2.923	-1.7086	2.0645	0.0629	0.111	0.2978	0.1005	0.1638	0.1637	-0.0764	-0.5496	-0.192	0.2065	0.0111	0.071	0.396	0.1516	0.3079	2.1656	29.9312	114.6911
13	3.7312	-1.069	0.8583	1.4073	-0.2525	0.9292	0.0723	0.253	0.1788	-0.0696	0.3102	0.5445	0.0179	-0.5879	-0.2423	0.2316	-0.026	0.0351	0.6335	0.2581	0.4564	-3.056	29.9284	99.7497
14	1.4326	0.3109	-0.3226	1.2729	-0.5712	1.7424	0.0664	0.3011	0.4203	-0.0043	0.2222	0.2705	-0.3556	-0.4391	-0.1262	0.2413	0.0677	0.0416	0.3796	0.182	0.4105	7.8465	41.761	97.9197
15	2	2	6.2161	2	2	9.9164	0.0838	0.4727	0.5557	0.8494	0.1841	-0.2268	-1.0989	0.0717	-0.2624	0.4911	0.0013	0.0744	0.1386	-0.0399	0.1232	51.0452	32.6148	142.3062
16	1.9999	2	-4.9898	2	1.9999	1.9999	-0.1758	-0.4357	-0.4787	-0.7381	0.6518	0.0452	0.4404	-0.5081	-0.4742	0.5236	-0.1119	0.0807	0.1882	-0.0055	0.1668	53.0758	11.448	98.2615
17	2	4.0876	3.6846	3.8407	2.5678	2.7234	-0.2257	0.6109	-0.5502	-0.9236	0.1805	0.5321	-0.0847	-0.0014	0.035	0.3783	-0.0782	-0.1533	0.2767	0.2244	0.6268	-4.5862	1.1665	129.5943
18	6.6104	5.2291	4.2265	4.8503	2.3908	3.9732	-0.5655	-0.6532	-0.2652	-0.6555	0.2	0.5966	-0.5155	0.6157	0.3414	0.5111	-0.0626	-0.0167	0.483	0.2365	0.668	-2.8674	43.7551	105.6163

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 446 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 69 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 70 through 117 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 118 through 161 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 163 through 446 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3 through 69 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 70 through 134 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 135 through 320 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 321 through 446 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 5 through 40 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 41 through 134 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 135 through 446 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 505 through 505 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 507 through 507 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 505 through 505 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 503 through 503 )

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