PDB-5f7x: Crystal structure of Mutant Q289L of adenosine/Methylthioadenosin...

ID or keywords:

Entry

Database: PDB / ID: 5f7x

Title

Crystal structure of Mutant Q289L of adenosine/Methylthioadenosine phosphorylase from Schistosoma mansoni in complex with Tubercidin

Components

Methylthioadenosine phosphorylase

Keywords

TRANSFERASE

Function / homology

Function and homology information

S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / nucleus / cytosol
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.77 Å

Authors

Torini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.M.

Funding support

Brazil, 2items

Citation

Journal: PLoS Negl Trop Dis / Year: 2016
Title: Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5'-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway.
Authors: Torini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.D.

History

Deposition	Dec 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 14, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3	Apr 17, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	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	5f7x.cif.gz	359 KB	Display	PDBx/mmCIF format
PDB format	pdb5f7x.ent.gz	290 KB	Display	PDB format
PDBx/mmJSON format	5f7x.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/5f7x ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7x	HTTPS FTP

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Related structure data

Related structure data	4l5aSC 4l5cC 4l5yC 4l6iC 5f73C 5f76C 5f77C 5f78C 5f7jC 5f7oC 5f7zC 5fakC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4l6i-1 5fak-1 5f7j-1 5f7j-2 5fak-2 4l5a-2 4l6i-2 1v45-1 5f76-d 4l5y-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Methylthioadenosine phosphorylase

B: Methylthioadenosine phosphorylase

C: Methylthioadenosine phosphorylase

hetero molecules

107 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	74.360, 81.900, 81.730
Angle α, β, γ (deg.)	90.00, 102.16, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Methylthioadenosine phosphorylase Mass: 35244.508 Da / Num. of mol.: 3 / Fragment: Enzyme / Mutation: Q289L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: I0B503, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical	ChemComp-TBN / '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 7-DEAZAADENOSINE Mass: 266.253 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₁₄N₄O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 944 / 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: 2.3 Å³/Da / Density % sol: 46.52 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM Bris-tris or Mes, 14-18% PEG3350, pH 6.5 / PH range: 6.1-6.7

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04-1 / Wavelength: 0.92 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.92 Å / Relative weight: 1

Reflection

Resolution: 1.77→48.89 Å / Num. obs: 90698 / % possible obs: 97.3 % / Redundancy: 3.8 % / B_iso Wilson estimate: 20.19 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 10.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Rejects	% possible all
1.77-1.82	3.7	0.57	1	0	89.6
7.92-48.89	3.8	0.044	1	0	95.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
xia2		data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L5A

4l5a

Resolution: 1.77→48.886 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1923	4547	5.01 %	Random selection
R_work	0.1637	-	-	-
obs	0.1651	90672	97.12 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.77→48.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6467	0	72	944	7483

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6694
X-RAY DIFFRACTION	f_angle_d	0.859	9089
X-RAY DIFFRACTION	f_dihedral_angle_d	11.677	3965
X-RAY DIFFRACTION	f_chiral_restr	0.058	1055
X-RAY DIFFRACTION	f_plane_restr	0.006	1153

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 (%)
1.77-1.7901	0.2614	138	0.2345	2544	X-RAY DIFFRACTION	87
1.7901-1.8112	0.3023	129	0.2274	2717	X-RAY DIFFRACTION	91
1.8112-1.8333	0.2571	152	0.2181	2667	X-RAY DIFFRACTION	92
1.8333-1.8565	0.2558	140	0.2084	2811	X-RAY DIFFRACTION	94
1.8565-1.8809	0.2563	156	0.2111	2707	X-RAY DIFFRACTION	95
1.8809-1.9067	0.2394	143	0.2045	2886	X-RAY DIFFRACTION	96
1.9067-1.9339	0.248	175	0.1984	2772	X-RAY DIFFRACTION	96
1.9339-1.9628	0.2171	167	0.1898	2855	X-RAY DIFFRACTION	97
1.9628-1.9935	0.2218	127	0.1774	2930	X-RAY DIFFRACTION	98
1.9935-2.0261	0.2124	147	0.179	2886	X-RAY DIFFRACTION	99
2.0261-2.0611	0.2083	140	0.1734	2910	X-RAY DIFFRACTION	99
2.0611-2.0986	0.1982	162	0.1652	2949	X-RAY DIFFRACTION	99
2.0986-2.1389	0.2037	160	0.1686	2908	X-RAY DIFFRACTION	99
2.1389-2.1826	0.2075	155	0.1679	2881	X-RAY DIFFRACTION	99
2.1826-2.23	0.1935	149	0.1635	2835	X-RAY DIFFRACTION	96
2.23-2.2819	0.1977	134	0.1616	2844	X-RAY DIFFRACTION	96
2.2819-2.339	0.2144	167	0.1606	2938	X-RAY DIFFRACTION	100
2.339-2.4022	0.1926	163	0.1571	2922	X-RAY DIFFRACTION	99
2.4022-2.4729	0.1936	163	0.1632	2921	X-RAY DIFFRACTION	99
2.4729-2.5527	0.2153	159	0.1593	2913	X-RAY DIFFRACTION	99
2.5527-2.6439	0.1923	154	0.1558	2957	X-RAY DIFFRACTION	99
2.6439-2.7498	0.1796	164	0.1593	2896	X-RAY DIFFRACTION	99
2.7498-2.8749	0.179	142	0.1597	2953	X-RAY DIFFRACTION	99
2.8749-3.0265	0.2076	155	0.1691	2927	X-RAY DIFFRACTION	99
3.0265-3.2161	0.188	153	0.1665	2883	X-RAY DIFFRACTION	97
3.2161-3.4643	0.1785	151	0.1582	2877	X-RAY DIFFRACTION	97
3.4643-3.8128	0.1826	147	0.1487	2960	X-RAY DIFFRACTION	99
3.8128-4.3643	0.1749	136	0.1363	2997	X-RAY DIFFRACTION	99
4.3643-5.4973	0.1415	174	0.1468	2949	X-RAY DIFFRACTION	99
5.4973-48.9044	0.1736	145	0.1692	2930	X-RAY DIFFRACTION	96

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	3.5034	-1.6218	-0.9381	2.3889	-1.5194	3.1295	-0.189	-0.0714	-0.2226	0.263	0.0604	0.7311	0.1621	-0.2796	0.1852	0.4052	-0.0067	0.1353	0.2645	-0.0685	0.3122	-25.4421	22.4007	122.6032
2	1.177	-0.55	-0.4051	1.3253	-0.0464	1.0791	0.0867	-0.1431	0.1707	0.2313	-0.0781	0.18	-0.285	-0.1289	-0.0124	0.2945	0.0275	0.0577	0.1813	-0.0269	0.1839	-20.3572	24.6823	116.0979
3	1.7208	0.3996	-0.4908	1.5013	-0.1455	2.1949	0.0908	-0.2327	-0.0489	0.2295	-0.0819	0.028	-0.0436	0.1585	0.0078	0.1634	0.0089	0.0023	0.1695	0.0185	0.1124	-9.7618	9.9856	117.3057
4	1.3914	-0.0598	-0.2638	1.2427	0.5327	2.6096	0.0324	-0.1635	-0.0293	0.1762	-0.0499	0.103	-0.0074	-0.1124	0.0261	0.1864	0.0076	0.0201	0.1478	0.0402	0.1316	-13.5997	11.8287	114.3144
5	1.8927	1.8278	-0.0611	4.6025	-0.8815	0.2388	0.3069	-0.3633	0.4967	0.6449	-0.1371	0.0774	-0.4404	0.071	-0.2068	0.2848	-0.0471	0.0101	0.2679	-0.0332	0.3068	22.118	37.5545	101.1678
6	2.0026	0.3614	0.3656	0.8969	0.0313	0.73	0.0534	-0.0436	0.2002	0.039	-0.0324	0.0346	-0.0975	0.031	-0.0176	0.1544	-0.0188	0.0197	0.149	-0.0034	0.1762	12.4137	28.6447	96.4915
7	2.4212	0.4898	-0.2792	0.7396	-0.239	0.9303	0.0767	-0.2239	-0.1398	0.0832	-0.0853	-0.15	-0.007	0.1169	0.0146	0.135	-0.0178	-0.0111	0.1394	-0.0001	0.1675	19.2733	19.4019	101.4083
8	3.0906	-0.7788	2.9487	1.5695	0.0672	3.4617	0.0003	0.5702	0.1944	-0.4296	-0.0841	0.0097	-0.2311	0.1332	0.0981	0.2554	0.0293	-0.0032	0.2002	-0.0114	0.169	-14.191	13.1588	68.4309
9	1.4366	-0.3949	-0.1254	1.8619	0.0767	0.6982	0.0399	0.1893	0.0296	-0.1357	-0.0384	0.092	-0.0891	-0.0558	0.005	0.1393	-0.0024	-0.0062	0.1089	0.0057	0.0874	-11.7902	14.2908	77.927
10	1.1245	-0.5796	-0.5711	2.2562	1.2458	2.1429	-0.0193	-0.0052	-0.1207	0.0323	-0.0183	0.142	-0.0276	-0.0439	0.023	0.1192	-0.0053	-0.0227	0.1101	0.0244	0.1307	-14.3075	5.5386	85.3396
11	0.9842	0.9488	0.1672	2.1187	1.3058	2.2291	0.0848	0.0015	-0.1328	0.1405	0.0123	-0.1463	0.1589	0.1202	-0.1108	0.1259	0.0206	-0.0281	0.141	-0.007	0.1814	3.0939	3.7785	86.9212
12	3.0004	-0.6369	0.2163	2.2381	0.2315	1.7382	0.0292	0.0105	-0.0514	-0.0188	0.0083	-0.2586	-0.0242	0.2065	-0.0452	0.1349	-0.0033	-0.0033	0.09	-0.0002	0.135	-4.5964	7.8204	84.2723
13	2.2153	0.0622	-0.2007	1.6313	0.3241	1.7471	0.0237	0.2028	-0.0675	-0.0412	-0.0257	0.0642	0.0512	-0.2234	0.0134	0.1459	0.0275	-0.0465	0.0301	0.0167	0.1753	-16.4226	5.8222	78.028

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 90 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 91 through 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 291 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 26 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 27 through 139 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 140 through 291 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3 through 23 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 24 through 110 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 111 through 164 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 165 through 198 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 199 through 243 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 244 through 294 )

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