PDB-6s2q: Mycobacterial hydrolase 1

ID or keywords:

Entry

Database: PDB / ID: 6s2q

Title

Mycobacterial hydrolase 1

Components

Glucosyl-3-phosphoglycerate phosphatase

Keywords

HYDROLASE / Mycobacterium tuberculosis / phosphatase

Function / homology

Function and homology information

glucosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity / dephosphorylation / phosphatase activity / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

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

Funding support

Portugal, 1items

Citation

Journal: to be published
Title: Mycobacterial hydrolase 1
Authors: Cereija, T.B. / Empadinhas, N. / Macedo-Ribeiro, S. / Pereira, P.J.B.

History

Deposition	Jun 21, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6s2q.cif.gz	341.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6s2q.ent.gz	280.9 KB	Display	PDB format
PDBx/mmJSON format	6s2q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6s2q_validation.pdf.gz	461.2 KB	Display	wwPDB validaton report
Full document	6s2q_full_validation.pdf.gz	470.2 KB	Display
Data in XML	6s2q_validation.xml.gz	37.3 KB	Display
Data in CIF	6s2q_validation.cif.gz	48.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/6s2q ftp://data.pdbj.org/pub/pdb/validation_reports/s2/6s2q	HTTPS FTP

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Related structure data

Similar structure data	5tl4-1 2pfn-d 4qza-d 4qzg-d 1smi-2 5mmh-2 4hvm-2 4e77-d 1g0s-d 2qzg-d Search similar-shape structures by Omokage search (details) 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/697 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#257 - May 2021 Fetal Hemoglobin similarity (6) #50 - Feb 2004 Glycolytic Enzymes similarity (6) #225 - Sep 2018 Phytase similarity (1)

Deposited unit

A: Glucosyl-3-phosphoglycerate phosphatase

B: Glucosyl-3-phosphoglycerate phosphatase

C: Glucosyl-3-phosphoglycerate phosphatase

D: Glucosyl-3-phosphoglycerate phosphatase

hetero molecules

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

1

A: Glucosyl-3-phosphoglycerate phosphatase

B: Glucosyl-3-phosphoglycerate phosphatase

hetero molecules

defined by author
Evidence: gel filtration
53 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glucosyl-3-phosphoglycerate phosphatase

D: Glucosyl-3-phosphoglycerate phosphatase

hetero molecules

defined by author
Evidence: gel filtration
52.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.955, 46.103, 103.247
Angle α, β, γ (deg.)	90.00, 104.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glucosyl-3-phosphoglycerate phosphatase / Mannosyl-3-phosphoglycerate phosphatase Mass: 25730.990 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: gpgP, Rv2419c / Production host: Escherichia coli (E. coli) References: UniProt: P9WIC7, glucosyl-3-phosphoglycerate phosphatase, mannosyl-3-phosphoglycerate phosphatase
#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: MES pH 6.0, sodium iodide, PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.5498 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5498 Å / Relative weight: 1
Reflection	Resolution: 2.5→50.03 Å / Num. obs: 27533 / % possible obs: 88.7 % / Redundancy: 12.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.025 / R_rim(I) all: 0.089 / R_sym value: 0.085 / Net I/σ(I): 26.1
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 7.8 % / R_merge(I) obs: 0.433 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1685 / CC_1/2: 0.911 / R_pim(I) all: 0.162 / R_rim(I) all: 0.464 / R_sym value: 0.433 / % possible all: 49.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
XDS		data reduction
Aimless		data scaling
Auto-Rickshaw		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→50.026 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2

	R_factor	Num. reflection	% reflection
R_free	0.2329	2532	4.8 %
R_work	0.1872	-	-
obs	0.1894	27521	87.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→50.026 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6450	0	23	172	6645

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6687
X-RAY DIFFRACTION	f_angle_d	1.109	9109
X-RAY DIFFRACTION	f_dihedral_angle_d	20.469	3945
X-RAY DIFFRACTION	f_chiral_restr	0.06	1002
X-RAY DIFFRACTION	f_plane_restr	0.007	1196

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 (%)
2.4999-2.5479	0.3024	61	0.2719	1363	X-RAY DIFFRACTION	43
2.5479-2.6	0.2702	82	0.2313	1645	X-RAY DIFFRACTION	53
2.6-2.6565	0.2663	104	0.2259	1929	X-RAY DIFFRACTION	60
2.6565-2.7183	0.2943	155	0.2275	2108	X-RAY DIFFRACTION	67
2.7183-2.7862	0.2747	143	0.2383	2450	X-RAY DIFFRACTION	79
2.7862-2.8616	0.3338	128	0.2308	2788	X-RAY DIFFRACTION	87
2.8616-2.9458	0.273	162	0.2247	3061	X-RAY DIFFRACTION	98
2.9458-3.0408	0.2762	142	0.2173	3238	X-RAY DIFFRACTION	100
3.0408-3.1495	0.2446	154	0.2163	3140	X-RAY DIFFRACTION	100
3.1495-3.2756	0.2326	152	0.2113	3186	X-RAY DIFFRACTION	100
3.2756-3.4246	0.2262	176	0.1925	3136	X-RAY DIFFRACTION	99
3.4246-3.6051	0.2357	155	0.1885	3161	X-RAY DIFFRACTION	100
3.6051-3.8309	0.2305	126	0.1701	3264	X-RAY DIFFRACTION	100
3.8309-4.1266	0.2047	177	0.1636	3071	X-RAY DIFFRACTION	99
4.1266-4.5416	0.2	187	0.1452	3145	X-RAY DIFFRACTION	100
4.5416-5.1982	0.2185	144	0.1567	3151	X-RAY DIFFRACTION	100
5.1982-6.5469	0.2323	135	0.1931	3224	X-RAY DIFFRACTION	100
6.5469-50.036	0.2076	149	0.1787	3160	X-RAY DIFFRACTION	100

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	0.603	1.0687	-0.4156	5.1309	0.3632	4.5824	0.0332	-0.1793	0.0298	0.3057	-0.008	-0.0722	-0.3012	-0.2144	-0.0215	0.1301	0.0114	0.0057	0.2197	0.0013	0.2432	0.3551	2.1228	14.791
2	8.0897	-4.3339	2.7945	5.9413	-0.1211	5.6863	-0.1759	0.1922	0.5126	-0.1426	-0.2009	0.5311	-0.17	-1.0711	-0.0241	0.2141	0.0156	-0.0047	0.4951	-0.0024	0.3883	-7.6654	3.1022	16.3908
3	3.1477	-0.4101	-0.3075	4.9749	0.0782	5.739	-0.1471	-0.6463	-0.2734	0.965	0.0528	0.1768	0.4189	-0.4544	0.0429	0.6048	-0.0279	0.0452	0.6446	-0.027	0.2267	2.4353	0.1937	41.8948
4	3.0311	-1.1712	0.7598	3.7737	0.0135	0.3346	0.1876	-0.7448	-0.1891	0.1129	-0.184	0.9067	-0.0654	-0.2151	0.1305	0.6318	0.1936	0.0584	1.0314	-0.1953	0.5685	-16.9146	12.1217	35.6439
5	1.7231	-0.1951	0.3235	4.7133	-0.5252	5.0726	0.0137	-0.5345	0.1758	0.3923	-0.1786	-0.3672	-0.6734	0.2164	0.1204	0.3876	0.0052	-0.0478	0.4127	-0.1135	0.3091	6.5673	9.6332	32.9246
6	7.6268	0.755	0.8376	8.9794	1.5313	6.8847	-0.1859	-0.1023	0.4268	-0.0219	0.0821	-0.8582	-0.865	0.563	0.0952	0.2999	-0.0235	-0.0204	0.2991	-0.0652	0.2854	8.9275	5.781	26.3722
7	4.6987	0.956	0.4702	4.9487	0.2496	4.0094	-0.1375	-0.2012	0.2097	0.1347	0.1234	0.1417	-0.7317	-0.0212	-0.0064	0.2605	0.0391	0.0015	0.2612	0.0441	0.2391	43.0602	-5.9385	8.8343
8	2.1185	-1.9627	0.4351	2.3695	-1.5653	2.559	0.0443	0.045	-0.0111	0.621	0.7562	1.2996	-0.9498	-0.8177	-0.3611	0.6219	0.1425	0.3083	0.3562	0.2627	1.2766	27.5793	-23.9859	10.432
9	2.1848	-0.9509	-0.0122	3.8918	0.2132	3.4813	-0.012	-0.0444	-0.1773	0.1889	-0.0974	-0.5704	0.1062	0.4972	0.0102	0.1401	0.011	-0.0331	0.3364	0.0483	0.3453	50.2376	-17.3862	11.214
10	4.6267	-0.2329	0.3955	4.4463	0.8525	5.2329	0.2074	-0.0022	-0.2328	-0.176	0.1064	-1.2554	0.4766	1.2939	-0.2881	0.3116	0.045	-0.0478	0.6346	0.1058	0.6633	58.9822	-18.7403	16.2645
11	6.325	2.0035	4.584	5.0891	2.0315	6.4199	-0.0102	-0.338	-0.0182	0.5768	-0.2561	-0.6312	-0.5558	0.5685	0.3269	0.5993	-0.0768	-0.1363	0.8047	0.1313	0.343	50.1044	-13.9211	37.3817
12	3.7907	-0.4804	1.1801	4.9038	0.8335	6.628	-0.2882	-0.516	0.255	0.3334	0.051	0.3585	-0.8224	0.0026	0.225	0.5181	0.0803	-0.046	0.658	0.0427	0.2719	47.6683	-13.1742	43.707
13	4.0653	1.154	1.2429	1.5886	1.1031	2.4604	0.1692	-0.2905	-0.28	-0.1866	-0.037	-0.412	0.197	0.7493	-0.1218	0.6107	0.2984	-0.0024	0.7772	0.0289	0.4361	66.7175	-26.1978	35.4264
14	3.2681	-0.9894	0.2869	5.539	0.6817	3.9007	-0.1189	-1.3981	-1.0757	0.1488	0.3247	1.2367	0.7053	-1.2201	-0.1432	0.4936	-0.1049	0.0279	0.825	0.1953	0.5434	36.857	-24.6442	37.4617
15	4.6301	-1.8685	0.5281	6.4922	1.5202	8.3529	0.072	-0.2637	-0.6392	-0.0538	-0.0846	0.6671	0.5103	-0.5107	0.0608	0.3267	0.014	-0.0485	0.3863	0.1101	0.3498	44.1551	-22.9505	29.7786
16	2.8882	-0.0454	-0.3355	3.8479	-0.3213	4.3824	0.1152	-0.1892	-0.2805	0.1045	-0.1035	-0.1038	0.747	0.097	0.0059	0.2488	-0.0314	-0.026	0.1609	0.0069	0.2002	3.9271	-10.5592	9.6962
17	2.8319	-1.2114	-0.6973	4.917	2.762	2.9339	-0.1117	-0.3114	0.598	1.1547	0.3047	-1.3335	0.2407	0.6814	-0.1103	0.3574	0.0139	-0.1102	0.255	-0.048	0.7131	17.7865	7.8958	6.2519
18	5.7404	0.2679	0.155	1.0849	-0.4016	3.5705	-0.0736	0.2209	1.1245	-0.1687	-0.1447	0.6302	-0.5807	-0.2616	0.1391	0.1854	0.0021	0.0121	0.2208	-0.0354	0.3087	-4.0288	3.1167	5.2913
19	4.4698	0.382	-0.5435	5.3521	0.6591	2.2864	-0.0602	-0.6554	-0.5476	0.2412	0.5782	2.7838	1.4877	-1.845	-0.5346	0.5768	-0.2052	0.1605	0.8781	0.0702	0.9451	-16.6253	-9.2409	15.4318

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 154 through 195 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 201 through 216 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 2 through 87 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 88 through 122 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 123 through 188 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 189 through 216 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 3 through 94 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 95 through 111 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 112 through 195 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 196 through 216 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 3 through 19 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 20 through 87 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 88 through 122 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 123 through 153 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 154 through 216 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 2 through 87 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 88 through 122 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 123 through 140 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 141 through 153 )

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