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

ID or keywords:

Entry

Database: PDB / ID: 5oiw

Title

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with glucosylglycerate

Components

Uncharacterized protein

Keywords

HYDROLASE / Mycobacterium

Function / homology

Function and homology information

glucosylglycerate hydrolase / glucosylglycerate hydrolase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation
Similarity search - Function

Biological species

Mycobacterium hassiacum

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.71 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 19, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 12, 2018	Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.2	May 15, 2019	Group: Data collection / Database references / Structure summary Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / 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 / _struct.title
Revision 1.3	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 2.0	Jul 29, 2020	Group: Atomic model / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5oiw.cif.gz	396.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5oiw.ent.gz	324.9 KB	Display	PDB format
PDBx/mmJSON format	5oiw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5oiw_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5oiw_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5oiw_validation.xml.gz	42.1 KB	Display
Data in CIF	5oiw_validation.cif.gz	64.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oi/5oiw ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oiw	HTTPS FTP

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Related structure data

Related structure data	5ohcC 5ohzSC 5oi0C 5oi1C 5oieC 5oivC 5oj4C 5ojuC 5ojvC 5ontC 5onzC 5oo2C 6q5tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5oju-1 5ojv-1 5oi1-1 5ohz-d 5oie-1 5ohc-1 5onz-1 5oo2-1 5oj4-1 5ont-1 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
Experimental dataset #1	Data reference: 10.15785/SBGRID/472 / 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: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

defined by author
Evidence: SAXS, gel filtration
207 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.292, 159.606, 91.043
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 / Sugars , 2 types, 4 molecules AB

#1: Protein	Uncharacterized protein Mass: 50913.484 Da / Num. of mol.: 2 / Mutation: D182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria) Gene: C731_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDL0
#5: Sugar	ChemComp-9WN / (2R)-2-(alpha-D-glucopyranosyloxy)-3-hydroxypropanoic acid / (2~{R})-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-propanoic acid / (2R)-2-(alpha-D-glucosyloxy)-3-hydroxypropanoic acid / (2R)-2-(D-glucosyloxy)-3-hydroxypropanoic acid / (2R)-2-(glucosyloxy)-3-hydroxypropanoic acid Type: D-saccharide / Mass: 268.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₉H₁₆O₉ / Feature type: SUBJECT OF INVESTIGATION

#1: Protein

Uncharacterized protein

Mass: 50913.484 Da / Num. of mol.: 2 / Mutation: D182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Gene: C731_0006 / Production host:

Escherichia coli (E. coli) / References: UniProt: K5BDL0

#5: Sugar

ChemComp-9WN / (2R)-2-(alpha-D-glucopyranosyloxy)-3-hydroxypropanoic acid / (2~{R})-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-propanoic acid / (2R)-2-(alpha-D-glucosyloxy)-3-hydroxypropanoic acid / (2R)-2-(D-glucosyloxy)-3-hydroxypropanoic acid / (2R)-2-(glucosyloxy)-3-hydroxypropanoic acid

Type: D-saccharide / Mass: 268.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₉H₁₆O₉ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 861 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 847 / 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: 3.05 Å³/Da / Density % sol: 59.71 %
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: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 1.71→49.1 Å / Num. obs: 133666 / % possible obs: 99.5 % / Redundancy: 6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.07 / R_pim(I) all: 0.031 / R_rim(I) all: 0.077 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.71→1.77 Å / Redundancy: 6.1 % / R_merge(I) obs: 1.081 / Mean I/σ(I) obs: 1.8 / CC_1/2: 0.659 / R_pim(I) all: 0.474 / R_rim(I) all: 1.183 / % possible all: 99

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OHZ

5ohz

Resolution: 1.71→45.934 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.52

	R_factor	Num. reflection	% reflection
R_free	0.1684	6717	5.03 %
R_work	0.1464	-	-
obs	0.1475	133615	99.29 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.71→45.934 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7160	0	125	847	8132

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7758
X-RAY DIFFRACTION	f_angle_d	1.025	10579
X-RAY DIFFRACTION	f_dihedral_angle_d	19.88	4573
X-RAY DIFFRACTION	f_chiral_restr	0.062	1085
X-RAY DIFFRACTION	f_plane_restr	0.008	1389

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 (%)
1.71-1.7294	0.2859	206	0.2777	4189	X-RAY DIFFRACTION	99
1.7294-1.7498	0.314	223	0.2634	4138	X-RAY DIFFRACTION	99
1.7498-1.7711	0.2695	206	0.251	4174	X-RAY DIFFRACTION	99
1.7711-1.7935	0.2965	236	0.2373	4173	X-RAY DIFFRACTION	99
1.7935-1.8171	0.258	228	0.229	4169	X-RAY DIFFRACTION	99
1.8171-1.842	0.2445	209	0.2208	4188	X-RAY DIFFRACTION	99
1.842-1.8684	0.2752	199	0.2115	4180	X-RAY DIFFRACTION	99
1.8684-1.8962	0.2183	240	0.1935	4215	X-RAY DIFFRACTION	99
1.8962-1.9259	0.2063	214	0.181	4124	X-RAY DIFFRACTION	99
1.9259-1.9574	0.1931	234	0.1742	4164	X-RAY DIFFRACTION	99
1.9574-1.9912	0.2192	208	0.1792	4211	X-RAY DIFFRACTION	99
1.9912-2.0274	0.2149	238	0.1566	4184	X-RAY DIFFRACTION	99
2.0274-2.0664	0.1802	230	0.1463	4203	X-RAY DIFFRACTION	100
2.0664-2.1086	0.158	238	0.1419	4193	X-RAY DIFFRACTION	99
2.1086-2.1544	0.1698	221	0.1434	4229	X-RAY DIFFRACTION	99
2.1544-2.2045	0.1635	189	0.1372	4214	X-RAY DIFFRACTION	100
2.2045-2.2597	0.1645	215	0.1386	4263	X-RAY DIFFRACTION	100
2.2597-2.3208	0.1647	235	0.1403	4214	X-RAY DIFFRACTION	100
2.3208-2.3891	0.1704	237	0.1393	4218	X-RAY DIFFRACTION	100
2.3891-2.4662	0.1784	230	0.1438	4222	X-RAY DIFFRACTION	100
2.4662-2.5543	0.1792	235	0.145	4242	X-RAY DIFFRACTION	100
2.5543-2.6566	0.1805	232	0.1438	4262	X-RAY DIFFRACTION	100
2.6566-2.7775	0.1562	208	0.1374	4210	X-RAY DIFFRACTION	98
2.7775-2.9239	0.1607	214	0.1387	4285	X-RAY DIFFRACTION	100
2.9239-3.107	0.163	217	0.1376	4270	X-RAY DIFFRACTION	100
3.107-3.3468	0.1487	214	0.1377	4307	X-RAY DIFFRACTION	100
3.3468-3.6835	0.1505	246	0.1313	4299	X-RAY DIFFRACTION	100
3.6835-4.2162	0.1318	219	0.116	4321	X-RAY DIFFRACTION	100
4.2162-5.3107	0.1374	241	0.1191	4342	X-RAY DIFFRACTION	99
5.3107-45.9508	0.1661	255	0.1636	4495	X-RAY DIFFRACTION	99

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	0.9779	-0.1016	0.2117	1.6102	-0.5225	1.8256	0.0133	0.1005	-0.0323	-0.1717	-0.0095	0.0211	0.023	-0.003	0.0044	0.144	0.01	0.0142	0.1479	-0.0118	0.1847	43.6071	14.8113	34.7967
2	4.9326	-3.1906	0.643	2.7929	-1.353	3.0286	0.12	0.1614	0.2106	-0.2456	-0.1762	-0.5147	-0.0794	0.4212	0.1896	0.1607	-0.0519	0.0305	0.2228	-0.0083	0.2155	58.068	22.4293	37.0262
3	4.7222	-0.4883	1.3487	0.5169	0.5556	3.0135	-0.0472	0.1623	0.379	-0.0587	0.0579	0.2229	-0.4381	-0.1126	-0.0051	0.2732	0.0639	-0.0032	0.1433	0.0465	0.2746	36.0161	36.0944	36.8052
4	0.6291	0.5956	-0.4923	4.9198	-1.9825	3.0453	0.0331	0.2268	0.186	-0.4194	0.0247	0.2562	-0.2204	-0.2468	-0.0552	0.2608	0.0841	-0.067	0.2718	0.0628	0.2857	29.7911	30.5842	26.3055
5	7.3396	-3.7741	-0.0235	3.5888	-0.0615	1.1563	-0.0684	-0.0242	0.3097	0.1354	0.0828	-0.1803	-0.3032	0.1784	-0.0197	0.236	-0.0597	0.0157	0.1398	0.0048	0.187	53.7004	32.2001	45.1749
6	3.0444	0.5811	0.9452	3.1981	-3.7692	5.9175	-0.0892	-0.1596	0.4668	0.2152	0.0909	0.3403	-0.8093	-0.3498	0.0091	0.4064	0.1346	0.0549	0.1802	-0.0142	0.3879	33.0815	41.5588	47.4028
7	1.0943	0.2412	0.2955	0.928	0.2154	1.3391	0.0266	-0.0777	0.0685	0.1106	-0.0084	0.2374	-0.129	-0.2157	-0.0121	0.157	0.0252	0.0398	0.1566	0.0131	0.2241	33.6626	21.3102	52.5885
8	1.3646	1.2717	1.4737	2.225	0.8038	3.1468	0.2113	-0.136	-0.1409	0.338	-0.1328	-0.0714	0.184	0.0619	-0.081	0.264	-0.0844	0.0124	0.2143	0.0202	0.1956	48.7104	6.5366	81.9417
9	2.1862	0.0225	1.3786	1.102	0.2267	3.2243	0.1601	-0.4779	0.0279	0.4609	-0.1768	-0.0098	-0.0247	-0.0166	0.0019	0.4142	-0.152	0.021	0.3009	-0.0021	0.1908	52.6661	18.9044	91.016
10	3.0936	0.1399	-0.0937	1.3301	0.0219	1.3982	0.1478	-0.3309	0.1379	0.3567	-0.1657	-0.0548	-0.2733	0.0966	0.0221	0.3952	-0.1191	0.0009	0.2566	-0.0041	0.1717	56.3515	26.3657	84.2264
11	1.3877	0.7854	0.7166	2.0024	1.1283	3.4873	0.1918	-0.4027	-0.0334	0.5567	-0.2253	-0.3453	-0.1389	0.3964	-0.0055	0.4799	-0.198	-0.1818	0.535	0.0961	0.3461	71.1698	17.2601	94.6483
12	6.7866	-0.3146	-0.7529	1.4962	0.0726	1.8035	0.1091	0.0304	0.3191	0.1909	-0.0973	0.0531	-0.4285	-0.0167	-0.0239	0.3662	-0.0708	0.0296	0.1898	-0.0272	0.1987	52.1816	32.6872	76.1667
13	1.3224	-0.1561	0.0538	1.5871	-0.2057	1.6628	0.0837	0.0144	0.0298	-0.0267	-0.1853	-0.2915	-0.1542	0.4467	0.0593	0.1874	-0.0672	-0.0089	0.2857	0.0293	0.255	69.6992	22.2561	66.5783
14	0.9787	-0.1729	0.4177	1.8105	-0.5264	2.0595	0.0972	-0.058	-0.1555	0.1226	-0.0646	-0.1459	0.125	0.1871	-0.0398	0.1826	-0.0338	-0.0191	0.1814	0.0051	0.215	59.8064	8.9136	71.1676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 134 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 135 through 162 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 163 through 193 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 194 through 249 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 250 through 297 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 298 through 320 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 321 through 446 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 69 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 70 through 134 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 135 through 193 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 194 through 249 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 250 through 297 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 298 through 365 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 366 through 446 )

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Yorodumi