PDB-6s2r: Mycobacterial hydrolase 2

ID or keywords:

Entry

Database: PDB / ID: 6s2r

Title

Mycobacterial hydrolase 2

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 /

MOLECULAR REPLACEMENT / Resolution: 1.45 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 2
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 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6s2r.cif.gz	210.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6s2r.ent.gz	168.1 KB	Display	PDB format
PDBx/mmJSON format	6s2r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6s2r_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	6s2r_full_validation.pdf.gz	456.1 KB	Display
Data in XML	6s2r_validation.xml.gz	23.7 KB	Display
Data in CIF	6s2r_validation.cif.gz	35.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/6s2r ftp://data.pdbj.org/pub/pdb/validation_reports/s2/6s2r	HTTPS FTP

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Related structure data

Related structure data	6s2qS S: Starting model for refinement
Similar structure data	5m8k-d 5m8j-d 6jbo-d 5m87-d 6tl2-d 4kld-d 4klf-d 4o5k-d 4be5-d 3at7-d 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/696 / 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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	98.953, 48.830, 93.477
Angle α, β, γ (deg.)	90.00, 104.33, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Glucosyl-3-phosphoglycerate phosphatase / Mannosyl-3-phosphoglycerate phosphatase Mass: 25730.990 Da / Num. of mol.: 2 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.13 Å³/Da / Density % sol: 42.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Calcium chloride dihydrate, PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97718 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97718 Å / Relative weight: 1
Reflection	Resolution: 1.45→47.51 Å / Num. obs: 75999 / % possible obs: 99 % / Redundancy: 4.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.043 / R_rim(I) all: 0.093 / R_sym value: 0.082 / Net I/σ(I): 8.4
Reflection shell	Resolution: 1.45→1.47 Å / Redundancy: 4.4 % / R_merge(I) obs: 1.427 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3740 / CC_1/2: 0.506 / R_pim(I) all: 0.739 / R_rim(I) all: 1.614 / R_sym value: 1.427 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6S2Q

6s2q

Resolution: 1.45→47.508 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.57

	R_factor	Num. reflection	% reflection
R_free	0.1999	3676	4.84 %
R_work	0.1739	-	-
obs	0.1752	75972	98.88 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→47.508 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3576	0	15	462	4053

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3860
X-RAY DIFFRACTION	f_angle_d	1.033	5270
X-RAY DIFFRACTION	f_dihedral_angle_d	24.765	1405
X-RAY DIFFRACTION	f_chiral_restr	0.089	571
X-RAY DIFFRACTION	f_plane_restr	0.007	700

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 (%)
1.45-1.4691	0.3663	149	0.312	2722	X-RAY DIFFRACTION	99
1.4691-1.4892	0.3189	143	0.2896	2789	X-RAY DIFFRACTION	99
1.4892-1.5105	0.2911	137	0.2693	2727	X-RAY DIFFRACTION	99
1.5105-1.533	0.2848	148	0.2568	2812	X-RAY DIFFRACTION	99
1.533-1.557	0.2891	133	0.2526	2718	X-RAY DIFFRACTION	99
1.557-1.5825	0.2856	143	0.251	2797	X-RAY DIFFRACTION	99
1.5825-1.6098	0.2771	141	0.2491	2740	X-RAY DIFFRACTION	99
1.6098-1.6391	0.3204	129	0.2671	2770	X-RAY DIFFRACTION	98
1.6391-1.6706	0.3081	138	0.261	2794	X-RAY DIFFRACTION	98
1.6706-1.7047	0.2572	140	0.2306	2711	X-RAY DIFFRACTION	99
1.7047-1.7418	0.2848	144	0.2181	2772	X-RAY DIFFRACTION	98
1.7418-1.7823	0.2293	124	0.2117	2749	X-RAY DIFFRACTION	98
1.7823-1.8269	0.2074	143	0.1962	2758	X-RAY DIFFRACTION	98
1.8269-1.8763	0.2307	141	0.1812	2762	X-RAY DIFFRACTION	98
1.8763-1.9315	0.2006	141	0.1755	2745	X-RAY DIFFRACTION	99
1.9315-1.9938	0.1925	147	0.1735	2760	X-RAY DIFFRACTION	99
1.9938-2.0651	0.2078	137	0.1724	2811	X-RAY DIFFRACTION	100
2.0651-2.1478	0.2063	133	0.1694	2816	X-RAY DIFFRACTION	100
2.1478-2.2455	0.1909	141	0.1645	2793	X-RAY DIFFRACTION	99
2.2455-2.3639	0.2023	132	0.1603	2796	X-RAY DIFFRACTION	99
2.3639-2.512	0.1936	157	0.1645	2793	X-RAY DIFFRACTION	99
2.512-2.7059	0.1865	153	0.1664	2794	X-RAY DIFFRACTION	100
2.7059-2.9782	0.2092	147	0.1675	2791	X-RAY DIFFRACTION	99
2.9782-3.409	0.1555	159	0.1504	2825	X-RAY DIFFRACTION	99
3.409-4.2946	0.1705	149	0.1357	2825	X-RAY DIFFRACTION	99
4.2946-47.5334	0.1721	127	0.1657	2926	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	2.3927	-3.0963	-3.0261	8.3923	-0.2158	8.5337	-0.3213	-0.619	-0.2561	1.3645	-0.0003	-0.183	-0.0404	-0.0432	0.2046	0.3554	-0.0233	-0.0364	0.3311	0.0389	0.315	-22.0061	45.6006	32.2446
2	1.4625	0.0111	-0.3212	2.8915	2.8224	3.988	-0.0874	0.0655	0.0432	-0.1334	0.0453	0.0678	-0.0093	-0.0944	0.0613	0.098	0.0031	-0.0144	0.1516	0.0167	0.1591	-14.7062	13.0147	13.6833
3	4.4182	1.1887	1.726	6.8304	5.0635	3.9233	-0.0124	0.2008	0.4774	-0.2191	0.0795	0.1138	-0.5104	-0.0593	-0.125	0.2794	-0.0363	-0.0616	0.1778	0.0631	0.3053	-10.5735	25.2918	15.1356
4	3.0225	1.5087	1.9917	1.7851	1.2853	3.2046	-0.1167	0.1375	0.0307	-0.1478	0.1067	-0.082	-0.1259	0.1817	-0.0096	0.1281	0.0163	0.0211	0.1769	-0.0095	0.1603	-10.7576	10.4333	13.6581
5	6.3128	-0.8977	3.682	0.4265	-0.67	2.4129	0.0402	0.4815	-0.2664	-0.0831	0.0504	0.0821	0.1379	-0.1644	-0.0623	0.1971	-0.0456	-0.0065	0.2291	-0.0261	0.1911	-26.8095	-1.1539	10.1451
6	7.0594	5.4742	4.8671	7.0241	5.7419	6.4324	0.0066	-0.1133	-0.1715	0.0663	0.023	-0.0613	0.1351	0.1319	-0.0503	0.1163	0.0151	0.0173	0.1605	0.04	0.1652	-14.9813	2.9176	25.9778
7	5.0284	-1.6591	-0.4867	5.9929	-1.4499	8.4892	-0.0827	-0.8737	0.5651	1.1915	-0.0267	-0.4955	-0.5856	0.539	0.0802	0.2789	-0.0409	-0.0824	0.3696	-0.0769	0.2384	-8.0947	18.4432	36.5662
8	2.2046	0.4865	-0.1674	1.9182	0.2203	0.6799	0.0017	0.0322	0.0114	0.0307	0.0044	0.0623	0.0241	0.034	-0.0058	0.1397	0.0167	-0.0109	0.172	0.0002	0.1693	-21.0546	11.2012	23.3204
9	3.4768	-1.9205	1.2653	5.4455	-1.2994	4.0132	-0.1768	-0.304	0.0927	0.4711	0.1796	0.0501	-0.1892	-0.0676	0.0309	0.1012	0.0192	0.0082	0.1927	-0.0318	0.1429	-20.3624	14.7403	29.9002
10	9.7018	1.5908	4.8196	9.403	7.2336	8.8407	0.2265	0.988	0.3716	-0.1794	0.0013	-1.0351	-0.4698	0.0352	-0.1601	0.8659	-0.0641	-0.1108	0.8194	0.2344	0.7663	-11.3429	28.0148	-1.4882
11	2.0973	0.6647	-0.4379	2.4653	-0.1287	1.4074	0.0108	-0.0178	0.053	0.0317	0.0221	0.1003	-0.1343	-0.0412	-0.0587	0.1187	0.0193	-0.0034	0.1393	0.0107	0.1835	-36.7916	32.6346	23.5822
12	1.327	0.5103	3.1355	1.1541	0.5407	7.694	-0.0033	-0.0649	0.0813	0.1804	0.0109	-0.1117	0.5053	0.2644	0.0416	0.3006	0.0444	0.0707	0.3168	0.0075	0.2485	-37.6668	21.1348	44.6238
13	2.3334	0.9329	-1.6477	2.9876	-1.5569	4.1624	-0.0888	0.4264	0.0144	-0.4143	0.0921	0.2589	0.2977	-0.5003	0.0041	0.1798	0.018	-0.047	0.2453	0.0162	0.2502	-43.7475	21.1667	14.7715
14	1.65	-0.7771	-0.386	3.469	-0.4225	2.4499	-0.0529	0.1218	-0.119	-0.186	0.0353	0.2286	0.1312	-0.1124	0.0491	0.0937	0.0025	-0.0075	0.1447	0.001	0.1597	-35.192	17.7708	21.1061

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 220 through 233 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1 through 31 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 48 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 49 through 101 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 122 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 123 through 140 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 141 through 153 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 154 through 196 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 197 through 219 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 220 through 234 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 87 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 88 through 122 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 123 through 153 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 154 through 219 )

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