PDB-5f76: Crystal structure of Mutant S12T of Adenosine/Methylthioadenosine...

ID or keywords:

Entry

Database: PDB / ID: 5f76

Title

Crystal structure of Mutant S12T of Adenosine/Methylthioadenosine Phosphorylase from Schistosoma mansoni in complex with Methylthioadenosine

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: 1.95 Å

Authors

Torini, J.R.S. / 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 7, 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: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen 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

-
Download

PDBx/mmCIF format	5f76.cif.gz	354.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5f76.ent.gz	286.7 KB	Display	PDB format
PDBx/mmJSON format	5f76.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5f76_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5f76_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5f76_validation.xml.gz	39.3 KB	Display
Data in CIF	5f76_validation.cif.gz	57.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/5f76 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f76	HTTPS FTP

-
Related structure data

Related structure data	4l5aSC 4l5cC 4l5yC 4l6iC 5f73C 5f77C 5f78C 5f7jC 5f7oC 5f7xC 5f7zC 5fakC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5fak-2 5fak-1 4l6i-1 4l5a-2 4l5y-2 5f7j-2 5f77-d 5f7z-2 5f7j-1 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

-
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)	76.810, 73.910, 81.290
Angle α, β, γ (deg.)	90.00, 102.44, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Methylthioadenosine phosphorylase Mass: 35273.508 Da / Num. of mol.: 3 / Fragment: Enzyme / Mutation: S12T 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-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE Mass: 297.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S
#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.: 742 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.23 %
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

-
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: 1.95→49.46 Å / Num. obs: 62658 / % possible obs: 96.8 % / Redundancy: 3.9 % / B_iso Wilson estimate: 21.98 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 9.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Rejects	% possible all
1.95-2	4	0.618	1	0	96.9
8.72-49.46	3.9	0.036	1	0	97.7

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L5A

4l5a

Resolution: 1.95→49.459 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.194	3172	5.06 %	Random selection
R_work	0.1663	-	-	-
obs	0.1677	62633	96.47 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→49.459 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6550	0	75	742	7367

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6782
X-RAY DIFFRACTION	f_angle_d	0.849	9209
X-RAY DIFFRACTION	f_dihedral_angle_d	14.634	4026
X-RAY DIFFRACTION	f_chiral_restr	0.054	1068
X-RAY DIFFRACTION	f_plane_restr	0.005	1172

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 (%)
1.95-1.9791	0.2803	147	0.2436	2576	X-RAY DIFFRACTION	96
1.9791-2.01	0.2445	126	0.2154	2588	X-RAY DIFFRACTION	97
2.01-2.043	0.2285	127	0.2056	2574	X-RAY DIFFRACTION	97
2.043-2.0782	0.2249	138	0.2011	2608	X-RAY DIFFRACTION	96
2.0782-2.116	0.2779	133	0.199	2600	X-RAY DIFFRACTION	97
2.116-2.1567	0.2199	146	0.1953	2550	X-RAY DIFFRACTION	96
2.1567-2.2007	0.2489	130	0.1958	2576	X-RAY DIFFRACTION	96
2.2007-2.2486	0.2196	126	0.1853	2343	X-RAY DIFFRACTION	88
2.2486-2.3009	0.224	145	0.1781	2506	X-RAY DIFFRACTION	95
2.3009-2.3584	0.1797	132	0.1709	2619	X-RAY DIFFRACTION	98
2.3584-2.4222	0.2198	138	0.1699	2628	X-RAY DIFFRACTION	98
2.4222-2.4935	0.1988	135	0.1787	2608	X-RAY DIFFRACTION	98
2.4935-2.5739	0.2242	127	0.174	2642	X-RAY DIFFRACTION	98
2.5739-2.6659	0.2096	139	0.1708	2627	X-RAY DIFFRACTION	98
2.6659-2.7727	0.1693	116	0.175	2631	X-RAY DIFFRACTION	98
2.7727-2.8988	0.2044	144	0.1692	2621	X-RAY DIFFRACTION	98
2.8988-3.0517	0.2202	166	0.178	2597	X-RAY DIFFRACTION	97
3.0517-3.2428	0.1927	133	0.1762	2459	X-RAY DIFFRACTION	91
3.2428-3.4931	0.2016	136	0.1615	2564	X-RAY DIFFRACTION	96
3.4931-3.8445	0.1692	140	0.1446	2670	X-RAY DIFFRACTION	98
3.8445-4.4006	0.1693	149	0.1313	2642	X-RAY DIFFRACTION	99
4.4006-5.5431	0.1474	161	0.1336	2622	X-RAY DIFFRACTION	97
5.5431-49.4748	0.1565	138	0.1544	2610	X-RAY DIFFRACTION	94

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	4.8953	-1.8229	0.0193	2.0035	-0.1033	2.481	0.0548	0.3164	-0.328	-0.2751	-0.0444	-0.3555	0.1073	0.4081	0.0153	0.1566	-0.0345	0.0529	0.2158	-0.0808	0.3232	40.7321	-16.907	8.3327
2	5.1299	2.1877	-1.4795	2.6575	-0.7736	2.369	0.0619	0.5006	0.0457	-0.2865	0.1913	-0.3888	-0.033	0.3596	-0.1964	0.2266	-0.022	0.0737	0.2643	-0.0736	0.3076	37.548	-24.7841	3.2229
3	0.8327	0.1234	-0.0145	1.4223	-0.0201	1.0044	-0.0423	0.0251	-0.0865	-0.0626	0.0633	-0.0925	-0.0332	0.1286	-0.0234	0.1203	-0.0068	0.0057	0.1455	-0.0387	0.1302	34.3848	-10.9494	14.4857
4	2.0159	-0.169	0.0379	1.0195	-0.2045	1.0046	-0.02	0.0685	0.022	-0.0875	0.0811	-0.0749	-0.0347	0.1063	-0.0513	0.1393	-0.0355	0.0117	0.1195	-0.0555	0.1349	31.8238	-9.2462	13.8368
5	1.2021	2.0496	-0.7404	3.5412	-1.5385	2.1262	-0.0129	-0.2534	-0.2201	0.1226	-0.0346	-0.2853	0.2651	0.2803	0.072	0.2314	0.0286	-0.0003	0.2383	0.0159	0.1162	11.3164	-30.3857	47.5654
6	0.664	0.2129	0.0247	0.7251	-0.1638	0.9374	0.0111	-0.0576	-0.0163	0.0708	0.0282	0.0236	-0.0281	-0.038	-0.039	0.1545	0.027	0.0155	0.1411	0.0328	0.129	10.8173	-18.3941	38.7065
7	0.479	-0.2051	0.2723	1.1007	-0.1939	1.876	-0.0126	-0.0351	-0.1063	0.1371	0.0695	0.001	-0.0148	0.0512	-0.0818	0.2173	0.0197	0.0266	0.1506	0.0173	0.1355	11.991	-17.8322	43.5843
8	0.7782	-0.1339	0.6039	1.3685	-0.0123	2.3047	-0.0657	0.4517	-0.3899	0.0351	0.0087	0.1439	0.1409	-0.5679	0.0323	0.1703	-0.0633	0.0369	0.3386	-0.0453	0.2793	-9.6749	-15.943	2.73
9	1.6987	0.0372	0.0658	1.8415	0.4001	1.1845	0.0103	0.3124	-0.111	-0.0455	-0.0005	0.2245	0.0835	-0.2664	-0.0146	0.1498	-0.0288	-0.0054	0.2519	0.0089	0.1898	-5.4099	-13.5072	4.7842
10	1.9796	-0.2672	-1.0518	1.6367	0.8256	1.4973	0.0331	0.0873	0.0292	0.0534	0.0334	-0.0127	0.0136	-0.0334	-0.0662	0.1369	0.0024	-0.0322	0.1197	0.04	0.1488	7.1819	-7.7459	10.0482
11	2.1947	-0.254	-0.268	1.5017	-0.0064	1.8056	0.0567	0.2179	0.7817	0.036	-0.0808	0.1941	-0.228	0.1189	-0.065	0.2155	0.0295	0.0251	0.2367	0.1385	0.4447	-5.9502	9.1935	7.3935
12	2.9615	-0.861	0.8683	1.3982	-1.3316	1.2626	-0.0386	-0.0932	0.3147	0.2257	-0.0003	0.1323	-0.2225	-0.0553	0.0392	0.1875	0.0321	0.0266	0.1361	-0.0043	0.2046	0.8244	0.0892	22.8156
13	1.6586	0.2234	0.0907	1.5956	0.2836	1.6423	0.002	-0.1066	0.1002	0.2043	0.0391	0.1636	-0.117	-0.1271	-0.0226	0.1899	0.0168	0.0147	0.1562	0.0312	0.2063	0.3491	-4.5173	15.3689
14	2.8883	-0.0328	-3.0039	1.0584	0.198	3.7629	-0.0359	0.1891	0.3281	-0.0019	-0.0008	-0.0286	0.4689	-0.3794	0.0678	0.1662	0.0218	-0.0143	0.2013	0.0243	0.3172	-15.5297	-2.1625	12.0081
15	6.2259	-2.9329	3.4656	4.0595	-2.8976	3.4408	0.1985	0.8053	0.0517	-0.4323	-0.1379	-0.0915	-0.0198	0.1926	-0.0469	0.3156	-0.0168	0.0386	0.2909	0.0198	0.1479	8.9184	-5.0747	-7.6477

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 292 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 23 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 24 through 220 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 221 through 291 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3 through 38 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 39 through 91 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 92 through 139 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 140 through 164 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 165 through 198 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 199 through 242 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 243 through 270 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 271 through 291 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi