PDB-6q5t: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat...

ID or keywords:

Entry

Database: PDB / ID: 6q5t

Title

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) - apo form

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: 2.54 Å

Authors

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

Funding support

Portugal, 2items

Organization	Grant number	Country
	Fundacao para a Ciencia e a Tecnologia (POCI-01-0145-FEDER-007274)	Portugal
	Norte Portugal Regional Operational Programme NORTE 2020 (Norte-01-0145-FEDER-000012)	Portugal

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	Dec 9, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 15, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2019	Group: Data collection / Database references / Category: pdbx_related_exp_data_set
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 1.3	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6q5t.cif.gz	379.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6q5t.ent.gz	312.6 KB	Display	PDB format
PDBx/mmJSON format	6q5t.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6q5t_validation.pdf.gz	432.4 KB	Display	wwPDB validaton report
Full document	6q5t_full_validation.pdf.gz	441.1 KB	Display
Data in XML	6q5t_validation.xml.gz	35.5 KB	Display
Data in CIF	6q5t_validation.cif.gz	51.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5t ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5t	HTTPS FTP

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Related structure data

Related structure data	5ohcC 5ohzSC 5oi0C 5oi1C 5oieC 5oivC 5oiwC 5oj4C 5ojuC 5ojvC 5ontC 5onzC 5oo2C 6g3n C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1z4z-1 1z50-1 3c4e-d 3tw0-d 3r25-6 9912 1z4y-1 6dde-d 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/641 / 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

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

1

A: hydrolase

B: hydrolase

A: hydrolase

B: hydrolase

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

Unit cell

Length a, b, c (Å)	167.008, 167.008, 243.266
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	180
Space group name H-M	P6₂22

Components on special symmetry positions

ID	Model	Components
1	1	B-557- HOH
2	1	B-702- HOH

#1: Protein	hydrolase Mass: 50957.496 Da / Num. of mol.: 2 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 379 / 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: 4.82 Å³/Da / Density % sol: 74.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: ADA pH 6.5, ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96863 Å / Relative weight: 1
Reflection	Resolution: 2.54→49.86 Å / Num. obs: 66272 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.109 / R_pim(I) all: 0.043 / R_rim(I) all: 0.117 / R_sym value: 0.109 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.54→2.63 Å / Redundancy: 7.3 % / R_merge(I) obs: 1.165 / Mean I/σ(I) obs: 1.8 / CC_1/2: 0.673 / R_pim(I) all: 0.459 / R_rim(I) all: 1.254 / R_sym value: 1.165 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OHZ

5ohz

Resolution: 2.54→49.86 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.77

	R_factor	Num. reflection	% reflection
R_free	0.2038	3359	5.08 %
R_work	0.1663	-	-
obs	0.1682	66183	99.63 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.54→49.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7088	0	0	379	7467

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7480
X-RAY DIFFRACTION	f_angle_d	1.058	10202
X-RAY DIFFRACTION	f_dihedral_angle_d	22.265	4403
X-RAY DIFFRACTION	f_chiral_restr	0.059	1050
X-RAY DIFFRACTION	f_plane_restr	0.007	1342

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 (%)
2.54-2.5763	0.3316	141	0.2974	2551	X-RAY DIFFRACTION	100
2.5763-2.6148	0.3619	146	0.2786	2577	X-RAY DIFFRACTION	100
2.6148-2.6556	0.3398	142	0.2751	2558	X-RAY DIFFRACTION	100
2.6556-2.6992	0.3102	126	0.2635	2587	X-RAY DIFFRACTION	99
2.6992-2.7457	0.2783	142	0.2456	2549	X-RAY DIFFRACTION	100
2.7457-2.7956	0.3082	120	0.2224	2609	X-RAY DIFFRACTION	100
2.7956-2.8494	0.2919	120	0.2286	2588	X-RAY DIFFRACTION	100
2.8494-2.9075	0.2582	150	0.2307	2579	X-RAY DIFFRACTION	100
2.9075-2.9708	0.3074	142	0.2318	2574	X-RAY DIFFRACTION	100
2.9708-3.0398	0.2867	125	0.228	2631	X-RAY DIFFRACTION	100
3.0398-3.1159	0.2931	139	0.2312	2572	X-RAY DIFFRACTION	100
3.1159-3.2001	0.24	136	0.2036	2601	X-RAY DIFFRACTION	100
3.2001-3.2942	0.2122	161	0.1799	2576	X-RAY DIFFRACTION	100
3.2942-3.4005	0.2146	139	0.1686	2605	X-RAY DIFFRACTION	100
3.4005-3.5221	0.2148	163	0.1648	2581	X-RAY DIFFRACTION	100
3.5221-3.663	0.1918	140	0.1419	2597	X-RAY DIFFRACTION	100
3.663-3.8297	0.1698	141	0.1284	2629	X-RAY DIFFRACTION	100
3.8297-4.0315	0.1565	161	0.1169	2604	X-RAY DIFFRACTION	100
4.0315-4.284	0.1489	139	0.1068	2657	X-RAY DIFFRACTION	100
4.284-4.6145	0.1335	116	0.1042	2658	X-RAY DIFFRACTION	100
4.6145-5.0785	0.1467	137	0.1143	2669	X-RAY DIFFRACTION	100
5.0785-5.8124	0.1629	147	0.1453	2687	X-RAY DIFFRACTION	100
5.8124-7.3193	0.2103	154	0.1708	2704	X-RAY DIFFRACTION	99
7.3193-49.8714	0.1831	132	0.1871	2881	X-RAY DIFFRACTION	98

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	7.8866	-3.5695	-6.1615	3.2183	4.1206	6.5879	0.0331	0.2614	-0.2952	0.0682	-0.3501	0.4188	-0.1295	-0.9147	0.3184	0.4124	0.0866	-0.0591	0.6173	0.0876	0.4293	18.8152	78.0327	33.354
2	8.4184	-0.9216	-4.2253	1.2453	0.2432	3.5283	0.1018	0.5217	0.2736	-0.1112	0.0714	0.1141	-0.433	-0.4373	-0.1595	0.4557	0.1199	0.0455	0.4798	0.1033	0.412	13.8857	87.8496	50.9005
3	8.1144	1.242	-6.2397	6.4753	-1.5847	7.9977	0.3809	-0.0401	0.5362	0.1737	-0.1337	-0.318	-0.7784	0.4649	-0.2372	0.3664	0.0094	-0.0407	0.362	0.0598	0.4669	29.9648	90.0004	52.5766
4	7.7729	2.4597	1.0565	4.3764	0.2913	3.7934	0.0211	-0.2075	-0.1412	0.4542	0.0349	0.1855	0.2368	-0.0778	-0.0153	0.4285	0.0798	0.1576	0.4303	0.0816	0.3437	13.3415	72.5212	63.1788
5	7.9703	3.8902	-7.2808	2.3564	-2.6829	8.5124	0.2001	1.2005	0.7482	-0.1528	-0.002	0.8446	-0.5656	-0.9106	-0.0496	0.6115	0.0685	0.0288	0.9138	0.0208	0.7767	-2.929	75.0545	53.1884
6	3.8122	0.1017	-0.7799	1.7973	-0.2363	2.0117	-0.0716	-0.3798	-0.0938	0.1674	0.0275	-0.0453	0.1595	0.0797	0.0439	0.4611	0.079	0.0523	0.4994	0.0414	0.2932	19.736	76.3788	64.7587
7	4.3385	0.6966	1.0722	2.3202	0.2518	4.2631	-0.1113	-0.0571	-0.2839	-0.0522	-0.0037	-0.0486	0.5846	0.1231	0.1121	0.3935	0.1069	0.094	0.3515	0.0452	0.3473	25.7385	64.0245	48.1316
8	4.1642	-1.7409	2.2608	2.9234	-0.7989	5.0425	-0.2491	-0.4309	0.2138	0.0277	0.0105	-0.2244	-0.3197	-0.0546	0.215	0.3241	0.101	0.0367	0.4795	0.0821	0.3701	25.0273	85.6325	23.2788
9	3.168	-1.0993	0.3763	5.0331	-0.7591	2.9196	-0.0197	-0.0119	-0.235	-0.1436	0.047	0.2681	0.2605	-0.1297	-0.0452	0.3416	0.0073	-0.034	0.3565	0.0491	0.3449	15.5447	83.5203	7.093
10	2.4309	0.7643	0.6396	4.2239	-1.0662	3.881	-0.066	0.1121	0.5373	0.0563	-0.0172	0.4617	-0.3679	-0.1978	0.0715	0.4712	0.0481	-0.0788	0.4189	0.0882	0.5247	22.5584	102.8943	2.1647
11	1.8637	-0.2548	-0.0191	2.4124	-0.6024	1.5795	0.0161	0.2049	-0.0064	-0.4304	-0.1242	-0.0935	0.1179	0.2265	0.1092	0.5621	0.0847	-0.0092	0.4786	0.0421	0.3084	26.5364	89.5806	-4.2309
12	2.0627	0.1877	-0.228	2.4815	0.227	2.73	0.0025	-0.1069	-0.1264	-0.0793	-0.1516	-0.2862	0.0979	0.5547	0.1445	0.3364	0.0794	-0.0066	0.4999	0.1053	0.3829	40.5366	90.3481	12.4672

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 162 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 163 through 193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 221 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 222 through 320 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 321 through 446 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 69 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 70 through 162 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 163 through 221 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 222 through 320 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 321 through 446 )

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