PDB-5f7o: Crystal structure of Mutant Q289L of adenosine/Methylthioadenosin...

ID or keywords:

Entry

Database: PDB / ID: 5f7o

Title

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

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 / Resolution: 1.8148 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	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Apr 17, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	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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Download

PDBx/mmCIF format	5f7o.cif.gz	361.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5f7o.ent.gz	292 KB	Display	PDB format
PDBx/mmJSON format	5f7o.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5f7o_validation.pdf.gz	474.7 KB	Display	wwPDB validaton report
Full document	5f7o_full_validation.pdf.gz	481.3 KB	Display
Data in XML	5f7o_validation.xml.gz	43.1 KB	Display
Data in CIF	5f7o_validation.cif.gz	65.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/5f7o ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7o	HTTPS FTP

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Related structure data

Related structure data	4l5aC 4l5cC 4l5yC 4l6iSC 5f73C 5f76C 5f77C 5f78C 5f7jC 5f7xC 5f7zC 5fakC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5f7z-2 5f78-2 5f73-1 5f77-d 4l5y-2 5f7z-1 5f73-2 5f78-1 4l5a-2 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
Related items in Molecule of the Month	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Methylthioadenosine phosphorylase

B: Methylthioadenosine phosphorylase

C: Methylthioadenosine phosphorylase

hetero molecules

106 kDa, 3 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)	74.354, 81.873, 81.760
Angle α, β, γ (deg.)	90.000, 101.950, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

Trimer confirmed by gel filtration

#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-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₅N₅
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1058 / 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: 46.56 %
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: 1.81→27.19 Å / Num. obs: 83708 / % possible obs: 96.7 % / Redundancy: 3.8 % / R_merge(I) obs: 0.121 / Net I/σ(I): 6.5 / Scaling rejects: 99

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Rejects	% possible all
1.81-1.91	3.8	0.536	1	0	97.8
5.74-27.19	4.3	0.061	1	0	98.2

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Processing

Software

Name	Version	Classification
xia2		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
xia2		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L6I

4l6i

Resolution: 1.8148→27.19 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2111	4158	4.99 %	Random selection
R_work	0.1821	79171	-	-
obs	0.1835	83329	96.13 %	-

Solvent computation

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

Displacement parameters

B_iso max: 78.01 Å² / B_iso mean: 25.2274 Å² / B_iso min: 5.95 Å²

Refinement step

Cycle: final / Resolution: 1.8148→27.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6482	0	30	1058	7570
B_iso mean	-	-	26.47	35.36	-
Num. residues	-	-	-	-	858

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6634
X-RAY DIFFRACTION	f_angle_d	0.656	9006
X-RAY DIFFRACTION	f_chiral_restr	0.049	1055
X-RAY DIFFRACTION	f_plane_restr	0.005	1150
X-RAY DIFFRACTION	f_dihedral_angle_d	11.609	3970

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8148-1.8354	0.2747	138	0.2598	2655	2793	97
1.8354-1.857	0.3126	135	0.2502	2698	2833	98
1.857-1.8796	0.2966	130	0.2441	2595	2725	97
1.8796-1.9034	0.3114	141	0.254	2722	2863	97
1.9034-1.9284	0.3835	143	0.3178	2581	2724	96
1.9284-1.9549	0.2995	128	0.2543	2609	2737	94
1.9549-1.9828	0.2384	117	0.2255	2522	2639	93
1.9828-2.0124	0.2536	125	0.2117	2310	2435	83
2.0124-2.0438	0.2317	117	0.2034	2482	2599	91
2.0438-2.0773	0.2892	140	0.1935	2670	2810	98
2.0773-2.1131	0.1813	146	0.1871	2660	2806	97
2.1131-2.1515	0.2323	135	0.1794	2724	2859	98
2.1515-2.1929	0.2225	134	0.188	2711	2845	99
2.1929-2.2376	0.2373	127	0.2053	2663	2790	97
2.2376-2.2862	0.327	164	0.2774	2578	2742	95
2.2862-2.3394	0.2	150	0.1798	2706	2856	99
2.3394-2.3979	0.2036	154	0.1767	2710	2864	99
2.3979-2.4627	0.2268	162	0.176	2690	2852	99
2.4627-2.5351	0.243	148	0.1778	2663	2811	98
2.5351-2.6168	0.2082	138	0.1736	2708	2846	98
2.6168-2.7103	0.2179	151	0.1731	2644	2795	97
2.7103-2.8187	0.1918	127	0.1671	2624	2751	94
2.8187-2.9468	0.196	121	0.1683	2301	2422	84
2.9468-3.102	0.2077	137	0.172	2721	2858	99
3.102-3.296	0.1988	148	0.1648	2738	2886	99
3.296-3.55	0.1567	150	0.16	2738	2888	99
3.55-3.9063	0.1491	153	0.15	2719	2872	99
3.9063-4.4694	0.1661	144	0.1347	2686	2830	97
4.4694-5.6228	0.1672	120	0.1522	2573	2693	92
5.6228-27.193	0.1831	135	0.1727	2770	2905	97

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	1.2715	-0.678	-0.115	1.2426	-0.0119	1.2633	0.0347	-0.2492	0.1729	0.2536	-0.0502	0.2381	-0.1288	-0.1285	-0.0164	0.2315	-0.0016	0.0683	0.1668	-0.0477	0.1867	52.9676	20.6993	118.1709
2	1.697	0.6232	-0.4262	1.3032	0.461	1.6416	0.0879	-0.3213	-0.0788	0.2798	-0.1122	0.0418	0.0648	0.1302	0.0203	0.1349	0.0007	-0.0003	0.1565	0.0215	0.1013	64.9792	6.5208	117.4361
3	1.3473	0.0201	0.0569	1.1773	0.6971	1.9452	0.0216	-0.2613	0.0033	0.2084	-0.0609	0.0747	0.0709	-0.0525	0.0279	0.1438	0.002	0.0129	0.1368	0.0264	0.0877	61.4241	8.4699	114.3914
4	4.3026	0.9853	-0.3688	1.6962	-0.4307	0.1142	0.2478	-0.2067	0.654	0.1997	-0.087	0.1039	-0.2272	0.1071	-0.1178	0.1937	-0.0518	0.0507	0.1577	-0.0423	0.2318	90.9452	33.4231	97.2549
5	1.5293	0.1119	-0.0957	0.576	-0.1518	0.8031	0.049	-0.2131	-0.0982	0.0517	-0.0569	-0.0927	0.0408	0.1122	0.0076	0.0994	-0.0239	-0.0138	0.13	0.0022	0.1657	89.8031	14.6948	101.7642
6	3.3547	0.6456	-0.3426	1.1066	-0.2787	0.7923	0.053	-0.0527	0.1251	0.0479	-0.0236	-0.0495	-0.1919	0.2353	-0.0331	0.1265	0.0115	0.0356	0.0543	0.003	0.1978	96.7578	22.3643	95.5445
7	2.828	-0.3918	2.6673	0.6145	-0.2832	2.6816	-0.162	0.5828	-0.0991	-0.4415	-0.0121	-0.1472	-0.0555	0.2872	0.1654	0.227	-0.0036	0.0054	0.175	-0.0431	0.123	60.8373	9.4211	68.6964
8	1.3015	-0.0293	0.0544	1.7454	0.1153	0.9941	0.0067	0.2247	0.0305	-0.1785	-0.0212	0.0706	-0.1237	-0.0576	0.0139	0.1167	0.0131	-0.0273	0.0986	0.0203	0.0838	59.4028	14.5099	75.7068
9	1.9953	-0.7224	-0.9961	1.4391	0.6715	1.637	0.0044	-0.0673	0.0398	0.0877	0.04	-0.0561	-0.0715	0.0281	-0.0353	0.0944	-0.009	-0.0271	0.0602	0.0186	0.0725	63.427	6.6504	89.7779
10	1.404	0.1924	-0.3112	1.7169	0.4702	1.2441	-0.049	0.0222	-0.3035	-0.0962	-0.0039	-0.0623	0.1439	0.0991	0.0298	0.1074	0.0002	-0.0098	0.0669	-0.0014	0.1412	68.014	-9.369	78.8778
11	1.5697	0.0859	0.0049	0.3158	0.0312	0.4665	0.0095	-0.059	0.0027	0.0413	-0.0098	-0.0526	-0.0072	0.0791	-0.0203	0.1093	-0.0021	-0.0142	0.0757	-0.0015	0.1122	72.1599	6.2561	89.4608
12	3.0728	-0.4901	-1.8503	0.4533	0.1952	2.0563	0.0649	-0.3254	0.4556	0.0485	-0.0138	-0.4471	-0.0496	0.3984	-0.1052	0.0866	-0.0013	0.0012	0.15	-0.0047	0.2929	75.749	2.97	77.9827
13	2.1454	1.9502	-0.556	2.0107	-0.2853	1.4299	-0.1117	0.2282	-0.0642	-0.2237	0.0767	-0.2066	0.0647	0.1454	0.0525	0.1643	0.0382	0.0061	0.0975	-0.0149	0.1455	70.8887	0.7445	68.3356
14	1.3003	-0.3615	-0.2021	2.5853	2.5298	6.169	0.0147	-0.1182	-0.0518	0.0891	-0.1344	0.3314	-0.0873	-0.7234	0.1627	0.0941	0.0047	-0.0011	0.1709	0.0118	0.2453	44.8634	3.9263	89.8585
15	2.0017	1.9999	2	2.0026	1.999	2.0023	0.7113	0.2086	0.1146	0.0902	-0.1632	-0.1202	-0.354	-0.498	-0.5338	0.3007	0.1008	0.0287	0.2647	0.0553	0.1215	57.4257	3.9213	105.3499

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 90 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 182 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 183 through 292 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 77 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 78 through 242 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 243 through 291 )	B
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 3 through 23 )	C
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 24 through 90 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 91 through 139 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 140 through 182 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 183 through 220 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 221 through 242 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 243 through 269 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 270 through 296 )	C
15	X-RAY DIFFRACTION	15	chain 'A' and resid 301	D

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