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

ID or keywords:

Entry

Database: PDB / ID: 5onz

Title

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

Components

Hydrolase

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: 1.93 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	Aug 4, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 29, 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	5onz.cif.gz	394.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5onz.ent.gz	324.5 KB	Display	PDB format
PDBx/mmJSON format	5onz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5onz_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5onz_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5onz_validation.xml.gz	40.6 KB	Display
Data in CIF	5onz_validation.cif.gz	60.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/on/5onz ftp://data.pdbj.org/pub/pdb/validation_reports/on/5onz	HTTPS FTP

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Related structure data

Related structure data	5ohcC 5ohzSC 5oi0C 5oi1C 5oieC 5oivC 5oiwC 5oj4C 5ojuC 5ojvC 5ontC 5oo2C 6q5tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6g3n-1 5oi1-1 5ohz-d 5ont-1 5oj4-1 5oie-1 5ojv-1 5oiv-1 5oiw-1 5oi0-1 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/482 / Data set type: diffraction image data / Details: data doi:10.15785/SBGRID/482

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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

hetero molecules

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

1

A: Hydrolase

B: Hydrolase

hetero molecules

A: Hydrolase

B: Hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.223, 158.901, 87.953
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Hydrolase 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
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Sugar	ChemComp-9YW / (alpha-D-glucopyranosyloxy)acetic acid / Glucosylglycolate / (alpha-D-glucosyloxy)acetic acid / (D-glucosyloxy)acetic acid / (glucosyloxy)acetic acid Type: D-saccharide / Mass: 238.192 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₄O₈ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SER / SERINE Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.97 Å³/Da / Density % sol: 58.56 %
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: ID23-2 / Wavelength: 0.8729 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 24, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8729 Å / Relative weight: 1
Reflection	Resolution: 1.93→48.67 Å / Num. obs: 91224 / % possible obs: 99.8 % / Redundancy: 6 % / CC_1/2: 0.994 / R_merge(I) obs: 0.126 / R_pim(I) all: 0.056 / R_rim(I) all: 0.139 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.93→2 Å / Redundancy: 6.2 % / R_merge(I) obs: 1.227 / Mean I/σ(I) obs: 1.5 / CC_1/2: 0.56 / R_pim(I) all: 0.533 / R_rim(I) all: 1.34 / % possible all: 98.7

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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: 1.93→48.668 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.08

	R_factor	Num. reflection	% reflection
R_free	0.1846	4566	5.01 %
R_work	0.1491	-	-
obs	0.1509	91157	99.74 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.93→48.668 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7160	0	152	677	7989

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7837
X-RAY DIFFRACTION	f_angle_d	0.984	10690
X-RAY DIFFRACTION	f_dihedral_angle_d	20.048	4617
X-RAY DIFFRACTION	f_chiral_restr	0.059	1097
X-RAY DIFFRACTION	f_plane_restr	0.007	1404

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 (%)
1.9305-1.9524	0.3077	134	0.2665	2773	X-RAY DIFFRACTION	96
1.9524-1.9754	0.3042	161	0.2644	2824	X-RAY DIFFRACTION	100
1.9754-1.9995	0.2744	150	0.249	2883	X-RAY DIFFRACTION	100
1.9995-2.0248	0.2515	147	0.2265	2826	X-RAY DIFFRACTION	100
2.0248-2.0514	0.2578	158	0.2243	2900	X-RAY DIFFRACTION	100
2.0514-2.0795	0.2471	176	0.2152	2781	X-RAY DIFFRACTION	100
2.0795-2.1092	0.248	150	0.2056	2876	X-RAY DIFFRACTION	100
2.1092-2.1407	0.2419	144	0.1943	2864	X-RAY DIFFRACTION	100
2.1407-2.1742	0.2204	146	0.1859	2854	X-RAY DIFFRACTION	100
2.1742-2.2098	0.2138	159	0.1673	2875	X-RAY DIFFRACTION	100
2.2098-2.2479	0.1949	156	0.1597	2835	X-RAY DIFFRACTION	100
2.2479-2.2888	0.2219	131	0.164	2895	X-RAY DIFFRACTION	100
2.2888-2.3328	0.2278	134	0.1575	2906	X-RAY DIFFRACTION	100
2.3328-2.3804	0.1784	143	0.1552	2868	X-RAY DIFFRACTION	100
2.3804-2.4322	0.2063	160	0.1537	2844	X-RAY DIFFRACTION	100
2.4322-2.4888	0.2148	163	0.1506	2871	X-RAY DIFFRACTION	100
2.4888-2.551	0.1818	157	0.1524	2873	X-RAY DIFFRACTION	99
2.551-2.62	0.198	141	0.1517	2891	X-RAY DIFFRACTION	100
2.62-2.697	0.185	156	0.142	2873	X-RAY DIFFRACTION	100
2.697-2.7841	0.1666	154	0.1392	2893	X-RAY DIFFRACTION	100
2.7841-2.8836	0.1768	136	0.1398	2891	X-RAY DIFFRACTION	100
2.8836-2.999	0.1527	169	0.1365	2887	X-RAY DIFFRACTION	100
2.999-3.1355	0.1891	140	0.1328	2900	X-RAY DIFFRACTION	100
3.1355-3.3008	0.1859	144	0.1357	2934	X-RAY DIFFRACTION	100
3.3008-3.5075	0.1694	136	0.1331	2906	X-RAY DIFFRACTION	100
3.5075-3.7782	0.1496	155	0.1198	2917	X-RAY DIFFRACTION	100
3.7782-4.1583	0.1541	173	0.1146	2916	X-RAY DIFFRACTION	100
4.1583-4.7595	0.1475	175	0.1134	2940	X-RAY DIFFRACTION	100
4.7595-5.9948	0.1727	163	0.1485	2969	X-RAY DIFFRACTION	100
5.9948-48.6832	0.1796	155	0.1663	3126	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	1.2309	0.6785	0.2593	4.9292	-1.1662	4.1838	-0.0402	0.067	-0.0962	-0.3474	0.0831	0.1227	0.1096	-0.1649	-0.0271	0.152	0.0119	-0.0131	0.1126	-0.0219	0.1754	42.2933	8.8749	37.5205
2	3.6469	-1.4508	2.2324	2.1016	-1.3428	4.9894	0.1745	0.367	-0.0191	-0.5427	-0.0995	0.029	-0.035	0.0516	-0.0975	0.32	-0.0019	0.023	0.1514	-0.0106	0.1835	46.5472	21.3106	28.2588
3	0.9938	0.0985	0.0122	1.2841	-0.0587	1.1153	-0.0146	0.0515	0.1651	-0.1358	0.014	0.1782	-0.2185	-0.0902	-0.0072	0.2189	0.0254	-0.0134	0.1385	0.0095	0.2167	39.4551	27.6374	41.9477
4	1.9455	1.4274	1.5286	2.2359	1.379	3.9491	0.2681	-0.4413	-0.0664	0.5549	-0.2615	-0.088	0.1041	0.1148	-0.0106	0.3097	-0.118	0.0052	0.3466	0.0371	0.183	52.5756	11.8698	86.8854
5	1.4728	0.2581	0.0629	1.3368	-0.0541	1.4615	0.1575	-0.3612	0.1051	0.3334	-0.1811	-0.195	-0.2521	0.2287	0.0477	0.3325	-0.1237	-0.0334	0.3168	-0.0183	0.2053	60.8713	24.9718	81.5476
6	1.0849	-0.0265	0.1086	2.429	-0.7478	2.0288	0.0581	-0.018	-0.1284	-0.0362	-0.1089	-0.2868	0.0179	0.2588	0.0361	0.1335	-0.024	-0.0062	0.1978	-0.0032	0.206	62.9479	11.9067	67.0201

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 446 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 117 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 118 through 320 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 321 through 446 )

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