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

ID or keywords:

Entry

Database: PDB / ID: 5ojv

Title

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) E419A variant in complex with mannosylglycerate

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: 2.062 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 24, 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 / 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 1.2	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.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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PDBx/mmCIF format	5ojv.cif.gz	383.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ojv.ent.gz	315 KB	Display	PDB format
PDBx/mmJSON format	5ojv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ojv_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5ojv_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5ojv_validation.xml.gz	38.1 KB	Display
Data in CIF	5ojv_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojv ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojv	HTTPS FTP

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Related structure data

Related structure data	5ohcC 5ohzSC 5oi0C 5oi1C 5oieC 5oivC 5oiwC 5oj4C 5ojuC 5ontC 5onzC 5oo2C 6q5tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5oiw-1 5oi1-1 5oie-1 5ohc-1 5oju-1 5oo2-1 5onz-1 6g3n-1 5ohz-d 5oiv-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/475 / 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

103 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&software
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)	87.792, 158.242, 87.589
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Uncharacterized protein Mass: 50899.461 Da / Num. of mol.: 2 / Mutation: E419A 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
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Sugar	ChemComp-2M8 / (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid / 2-O-ALPHA-MANNOSYL-D-GLYCERATE / (2R)-3-hydroxy-2-(alpha-D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(mannosyloxy)propanoic acid Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆O₉ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SER / SERINE Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 463 / 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 Å³/Da / Density % sol: 58.97 %
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: ID30B / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.06→48.805 Å / Num. obs: 74395 / % possible obs: 98 % / Redundancy: 6.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.086 / R_pim(I) all: 0.037 / R_rim(I) all: 0.094 / Net I/σ(I): 12.1
Reflection shell	Resolution: 2.06→2.13 Å / Redundancy: 6 % / R_merge(I) obs: 0.979 / Mean I/σ(I) obs: 1.5 / CC_1/2: 0.715 / R_pim(I) all: 0.423 / R_rim(I) all: 1.069 / % possible all: 89.3

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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: 2.062→48.805 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.95

	R_factor	Num. reflection	% reflection
R_free	0.1935	3733	5.02 %
R_work	0.1551	-	-
obs	0.1571	74327	97.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.062→48.805 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7158	0	97	463	7718

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7601
X-RAY DIFFRACTION	f_angle_d	0.985	10369
X-RAY DIFFRACTION	f_dihedral_angle_d	17.206	4466
X-RAY DIFFRACTION	f_chiral_restr	0.058	1073
X-RAY DIFFRACTION	f_plane_restr	0.007	1356

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 (%)
2.0617-2.0877	0.3059	111	0.3092	1934	X-RAY DIFFRACTION	73
2.0877-2.1152	0.3269	118	0.2675	2569	X-RAY DIFFRACTION	98
2.1152-2.1442	0.347	121	0.2598	2664	X-RAY DIFFRACTION	99
2.1442-2.1748	0.2965	162	0.2507	2579	X-RAY DIFFRACTION	99
2.1748-2.2073	0.2888	139	0.2319	2611	X-RAY DIFFRACTION	99
2.2073-2.2418	0.3189	138	0.2218	2581	X-RAY DIFFRACTION	99
2.2418-2.2785	0.2764	122	0.215	2571	X-RAY DIFFRACTION	97
2.2785-2.3178	0.2217	124	0.1963	2588	X-RAY DIFFRACTION	97
2.3178-2.36	0.2385	141	0.1977	2650	X-RAY DIFFRACTION	99
2.36-2.4054	0.2447	143	0.1827	2590	X-RAY DIFFRACTION	99
2.4054-2.4545	0.2574	142	0.1929	2657	X-RAY DIFFRACTION	99
2.4545-2.5078	0.2352	125	0.1804	2640	X-RAY DIFFRACTION	99
2.5078-2.5662	0.2272	135	0.1772	2630	X-RAY DIFFRACTION	99
2.5662-2.6303	0.2219	144	0.1697	2634	X-RAY DIFFRACTION	100
2.6303-2.7014	0.2171	162	0.1606	2636	X-RAY DIFFRACTION	100
2.7014-2.7809	0.2049	133	0.1635	2654	X-RAY DIFFRACTION	100
2.7809-2.8707	0.2336	146	0.1578	2651	X-RAY DIFFRACTION	100
2.8707-2.9733	0.1904	124	0.1552	2571	X-RAY DIFFRACTION	96
2.9733-3.0923	0.1984	145	0.1491	2651	X-RAY DIFFRACTION	99
3.0923-3.233	0.1728	138	0.1435	2692	X-RAY DIFFRACTION	100
3.233-3.4034	0.2068	140	0.1419	2658	X-RAY DIFFRACTION	100
3.4034-3.6166	0.162	161	0.1364	2653	X-RAY DIFFRACTION	99
3.6166-3.8957	0.1559	152	0.1264	2654	X-RAY DIFFRACTION	99
3.8957-4.2875	0.1502	148	0.1212	2642	X-RAY DIFFRACTION	97
4.2875-4.9075	0.1539	150	0.1203	2668	X-RAY DIFFRACTION	98
4.9075-6.1809	0.1902	138	0.1524	2735	X-RAY DIFFRACTION	100
6.1809-48.8184	0.1659	131	0.1555	2831	X-RAY DIFFRACTION	97

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	0.745	0.8252	0.2916	5.5639	-2.6519	4.0452	0.0179	0.0934	-0.0471	-0.3636	0.0525	0.2461	0.1009	-0.1375	-0.0584	0.2421	0.0125	-0.0001	0.2038	-0.0399	0.2473	43.0154	9.0506	37.3154
2	4.6889	-1.9406	3.1395	2.5634	-1.9048	6.1098	0.132	0.364	-0.0873	-0.5756	-0.051	0.019	-0.0321	-0.0315	-0.0886	0.3718	-0.0091	0.0254	0.1992	-0.0125	0.2461	47.0505	21.34	28.5052
3	5.2453	-2.6762	-0.2774	4.0793	0.1584	1.2814	0.0343	0.2753	0.3033	-0.3288	-0.0338	-0.1483	-0.3249	0.1188	-0.0014	0.3642	-0.0101	0.0126	0.2428	0.0205	0.1696	48.5504	29.478	35.1567
4	1.4729	0.8116	-0.898	4.8437	-2.372	4.2809	-0.0286	0.31	0.2706	-0.6271	0.0679	0.4441	-0.2222	-0.3773	-0.0764	0.4654	0.1002	-0.134	0.3712	0.0463	0.3762	30.8006	30.5392	24.8223
5	8.3134	-2.9777	-0.4225	2.9578	0.9153	1.5241	-0.097	-0.2466	0.3243	0.0262	0.059	0.0317	-0.3858	0.0724	0.0389	0.3782	-0.0129	0.0028	0.1768	0.0219	0.2484	48.6669	35.2718	44.279
6	1.981	0.1535	0.5179	2.0776	0.2187	1.6848	-0.0252	-0.0823	0.0801	0.0761	0.0156	0.3947	-0.1011	-0.21	0.0203	0.2097	0.0311	0.0361	0.234	0.0231	0.292	35.1244	21.4393	50.8688
7	1.6122	2.169	1.8161	4.7399	1.8295	5.5535	0.2991	-0.2891	-0.1869	0.5675	-0.2216	-0.1975	0.248	0.0011	-0.0745	0.2623	-0.0744	0.0075	0.3009	0.047	0.2722	50.111	6.7726	80.4099
8	3.5211	-0.0198	2.1965	1.2833	0.0452	5.0313	0.2869	-0.7559	-0.0442	0.4757	-0.2396	-0.0894	-0.0599	0.0179	-0.0515	0.4299	-0.1763	0.0256	0.4709	0.0235	0.2738	54.2218	18.9856	88.8886
9	6.4472	0.6481	-0.3709	2.1064	0.1135	1.7172	0.2101	-0.5576	0.2413	0.4042	-0.2066	-0.0622	-0.3902	0.0909	0.002	0.4366	-0.1151	0.0067	0.3761	-0.0175	0.1959	58.3897	26.0417	82.3727
10	1.3192	1.473	1.2409	3.3768	1.9698	4.2886	0.3721	-0.5468	-0.2957	0.7139	-0.3465	-0.539	0.0682	0.4563	-0.0678	0.5449	-0.2218	-0.2005	0.8488	0.1603	0.5423	73.0097	16.629	92.7377
11	4.8244	-0.324	-0.9654	1.87	-0.2717	1.9414	0.2596	-0.1388	0.2427	0.1856	-0.2268	-0.1693	-0.436	0.1948	-0.0197	0.4047	-0.1144	-0.0102	0.2698	-0.0199	0.2454	61.8632	31.0113	73.3279
12	1.7826	0.5147	0.0028	2.7538	-0.8344	2.3596	0.0685	-0.0749	-0.2816	0.0224	-0.1397	-0.371	0.0524	0.2118	0.0642	0.207	-0.025	-0.012	0.2602	0.0008	0.3179	64.0878	11.8483	66.8824

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 134 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 135 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 320 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 321 through 446 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 69 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 70 through 134 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 135 through 193 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 194 through 249 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 250 through 320 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 321 through 446 )

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