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

ID or keywords:

Entry

Database: PDB / ID: 5oiv

Title

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D43A variant in complex with serine and glycerol

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 DSM 44199 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.783 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	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.identifier_ORCID / _citation_author.name
Revision 1.3	Jan 17, 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	5oiv.cif.gz	398.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5oiv.ent.gz	328.1 KB	Display	PDB format
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Validation report

Summary document	5oiv_validation.pdf.gz	472 KB	Display	wwPDB validaton report
Full document	5oiv_full_validation.pdf.gz	479.9 KB	Display
Data in XML	5oiv_validation.xml.gz	41.1 KB	Display
Data in CIF	5oiv_validation.cif.gz	62.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oi/5oiv ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oiv	HTTPS FTP

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Related structure data

Related structure data	5ohcC 5ohzSC 5oi0C 5oi1C 5oieC 5oiwC 5oj4C 5ojuC 5ojvC 5ontC 5onzC 5oo2C 6q5tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5oie-1 5oi0-1 5oi1-1 5onz-1 5ont-1 5ohz-d 5ojv-1 5tht-d 6g3n-1 5oiw-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/471 / 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) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Hydrolase

B: Hydrolase

hetero molecules

103 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
207 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.921, 159.126, 88.161
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: D43A 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 Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SER / SERINE Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 761 / 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: 58.57 %
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: 0.96598 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: 0.96598 Å / Relative weight: 1
Reflection	Resolution: 1.78→48.67 Å / Num. obs: 114314 / % possible obs: 98.9 % / Redundancy: 4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.032 / R_rim(I) all: 0.066 / Net I/σ(I): 13
Reflection shell	Resolution: 1.78→1.85 Å / Redundancy: 4 % / R_merge(I) obs: 0.824 / Mean I/σ(I) obs: 1.7 / CC_1/2: 0.529 / R_pim(I) all: 0.472 / R_rim(I) all: 0.954 / % possible all: 93.5

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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: 1.783→45.45 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.33

	R_factor	Num. reflection	% reflection
R_free	0.1786	5735	5.02 %
R_work	0.1488	-	-
obs	0.1503	114235	98.82 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.783→45.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7160	0	101	761	8022

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7840
X-RAY DIFFRACTION	f_angle_d	1.009	10697
X-RAY DIFFRACTION	f_dihedral_angle_d	20.651	4630
X-RAY DIFFRACTION	f_chiral_restr	0.062	1085
X-RAY DIFFRACTION	f_plane_restr	0.008	1418

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 (%)
1.7833-1.8036	0.3513	159	0.2912	2931	X-RAY DIFFRACTION	81
1.8036-1.8248	0.271	187	0.2629	3607	X-RAY DIFFRACTION	100
1.8248-1.8471	0.2827	202	0.2499	3573	X-RAY DIFFRACTION	100
1.8471-1.8705	0.2735	188	0.2397	3636	X-RAY DIFFRACTION	100
1.8705-1.8951	0.2554	199	0.2304	3590	X-RAY DIFFRACTION	100
1.8951-1.921	0.2676	202	0.2236	3588	X-RAY DIFFRACTION	100
1.921-1.9485	0.2327	189	0.2273	3592	X-RAY DIFFRACTION	99
1.9485-1.9776	0.2676	180	0.2147	3590	X-RAY DIFFRACTION	99
1.9776-2.0085	0.2158	193	0.1856	3618	X-RAY DIFFRACTION	99
2.0085-2.0414	0.2117	195	0.1705	3563	X-RAY DIFFRACTION	99
2.0414-2.0766	0.2079	195	0.1636	3595	X-RAY DIFFRACTION	99
2.0766-2.1144	0.193	178	0.1578	3622	X-RAY DIFFRACTION	100
2.1144-2.155	0.1849	200	0.1567	3651	X-RAY DIFFRACTION	100
2.155-2.199	0.1876	207	0.1478	3614	X-RAY DIFFRACTION	100
2.199-2.2468	0.1997	199	0.1457	3597	X-RAY DIFFRACTION	100
2.2468-2.2991	0.1937	185	0.1497	3645	X-RAY DIFFRACTION	100
2.2991-2.3566	0.1815	177	0.145	3649	X-RAY DIFFRACTION	100
2.3566-2.4203	0.1833	223	0.1482	3609	X-RAY DIFFRACTION	100
2.4203-2.4915	0.1974	185	0.1455	3626	X-RAY DIFFRACTION	100
2.4915-2.5719	0.1546	192	0.1477	3665	X-RAY DIFFRACTION	100
2.5719-2.6638	0.1635	193	0.1426	3642	X-RAY DIFFRACTION	100
2.6638-2.7705	0.1857	191	0.1463	3643	X-RAY DIFFRACTION	100
2.7705-2.8966	0.1677	158	0.1454	3687	X-RAY DIFFRACTION	100
2.8966-3.0492	0.1671	201	0.1439	3623	X-RAY DIFFRACTION	98
3.0492-3.2402	0.1744	175	0.1415	3690	X-RAY DIFFRACTION	100
3.2402-3.4903	0.1887	175	0.1423	3668	X-RAY DIFFRACTION	99
3.4903-3.8414	0.144	196	0.1249	3705	X-RAY DIFFRACTION	99
3.8414-4.3969	0.1348	207	0.1133	3686	X-RAY DIFFRACTION	99
4.3969-5.538	0.1643	207	0.1276	3713	X-RAY DIFFRACTION	99
5.538-45.4648	0.1817	197	0.1619	3882	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	1.1136	1.0665	0.2031	5.1006	-1.7637	4.3934	-0.0154	0.0924	-0.0639	-0.2684	0.0594	0.2138	0.0399	-0.1615	-0.0289	0.1459	0.0228	-0.0005	0.1282	-0.0249	0.1955	41.9849	8.877	37.85
2	2.8444	-1.649	1.9631	3.1472	-1.9748	5.3107	0.1648	0.301	-0.0327	-0.5237	-0.1366	0.0611	-0.0585	0.0109	-0.0218	0.2584	-0.0053	0.0355	0.1726	-0.0193	0.1931	46.7748	21.1029	28.5855
3	1.0346	-0.0259	-0.0203	1.2466	-0.1498	1.0528	0.0232	0.0554	0.144	-0.1051	0.0027	0.1703	-0.2102	-0.0976	-0.0287	0.2145	0.0276	-0.0023	0.1472	0.0059	0.213	39.1605	27.7463	41.8587
4	2.86	3.4244	2.636	5.9131	2.0528	7.2405	0.2528	-0.1115	-0.2438	0.3945	-0.1217	-0.2255	0.5046	0.3371	-0.1341	0.1932	-0.0077	-0.0239	0.2198	0.0567	0.231	51.1166	1.1398	79.3424
5	2.9258	1.1397	2.2202	1.1232	1.5012	5.7569	0.3157	-0.6933	-0.0315	0.4735	-0.357	-0.0469	0.0482	0.1251	0.029	0.4193	-0.1481	0.0174	0.4239	0.011	0.2155	52.9943	17.8487	91.25
6	1.1812	0.327	-0.1081	1.4839	-0.0395	1.3376	0.1344	-0.2596	-0.011	0.2377	-0.1556	-0.2362	-0.1372	0.2476	0.01	0.2264	-0.0848	-0.0309	0.2788	0.0126	0.1975	61.3467	20.0225	76.1501

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 40 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 41 through 117 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 118 through 446 )

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