PDB-5f77: Crystal structure of Mutant S12T of adenosine/Methylthioadenosine...

ID or keywords:

Entry

Database: PDB / ID: 5f77

Title

Crystal structure of Mutant S12T 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 /

molecular replacement / Resolution: 2.02 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	Nov 1, 2017	Group: Author supporting evidence / Data collection Category: diffrn_source / pdbx_struct_assembly_auth_evidence Item: _diffrn_source.pdbx_synchrotron_site
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

-
Download

PDBx/mmCIF format	5f77.cif.gz	354.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5f77.ent.gz	287.9 KB	Display	PDB format
PDBx/mmJSON format	5f77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/5f77 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f77	HTTPS FTP

-
Related structure data

Related structure data	4l5aC 4l5cC 4l5yC 4l6iSC 5f73C 5f76C 5f78C 5f7jC 5f7oC 5f7xC 5f7zC 5fakC 5f75 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5f7z-2 5f7o-d 5f73-1 5fak-2 4l5y-2 5fak-1 4l6i-2 5f7z-1 4l5a-2 5f76-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

-
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

107 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)	74.460, 84.650, 75.920
Angle α, β, γ (deg.)	90.000, 106.280, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

Trimer confirmed by gel filtration

#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-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₅N₅
#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.: 647 / 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: 2.17 Å³/Da / Density % sol: 43.33 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / 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: 2.02→72.88 Å / Num. all: 58891 / Num. obs: 58891 / % possible obs: 99.2 % / Redundancy: 4.2 % / R_merge(I) obs: 0.086 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.02→2.07 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.615 / Mean I/σ(I) obs: 2.2 / % possible all: 99.1

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L6I

4l6i

Resolution: 2.02→72.876 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2151	2982	5.07 %	Random selection
R_work	0.1682	55886	-	-
obs	0.1706	58868	99.11 %	-

Solvent computation

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

Displacement parameters

B_iso max: 111.02 Å² / B_iso mean: 33.8822 Å² / B_iso min: 13.16 Å²

Refinement step

Cycle: final / Resolution: 2.02→72.876 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6542	0	45	647	7234
B_iso mean	-	-	43.42	39.41	-
Num. residues	-	-	-	-	858

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6721
X-RAY DIFFRACTION	f_angle_d	0.618	9122
X-RAY DIFFRACTION	f_chiral_restr	0.048	1051
X-RAY DIFFRACTION	f_plane_restr	0.005	1167
X-RAY DIFFRACTION	f_dihedral_angle_d	13.459	4003

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.02-2.0531	0.3032	159	0.2578	2615	2774	99
2.0531-2.0885	0.2764	172	0.2312	2616	2788	100
2.0885-2.1265	0.3002	137	0.2216	2680	2817	100
2.1265-2.1674	0.2632	137	0.2257	2712	2849	100
2.1674-2.2117	0.2704	132	0.2015	2654	2786	100
2.2117-2.2598	0.2516	141	0.1944	2702	2843	100
2.2598-2.3123	0.2703	146	0.1944	2629	2775	100
2.3123-2.3701	0.2446	141	0.1882	2661	2802	100
2.3701-2.4342	0.2373	118	0.1748	2673	2791	100
2.4342-2.5059	0.2315	134	0.175	2691	2825	100
2.5059-2.5868	0.2498	137	0.1739	2652	2789	99
2.5868-2.6792	0.2317	130	0.1677	2668	2798	99
2.6792-2.7865	0.2482	130	0.1694	2609	2739	98
2.7865-2.9133	0.2257	145	0.1692	2569	2714	95
2.9133-3.0669	0.2278	140	0.181	2663	2803	100
3.0669-3.2591	0.2268	162	0.1759	2688	2850	100
3.2591-3.5107	0.2206	143	0.1673	2668	2811	100
3.5107-3.864	0.1897	153	0.1497	2663	2816	99
3.864-4.423	0.1713	147	0.1298	2683	2830	99
4.423-5.5722	0.1567	121	0.1348	2642	2763	97
5.5722-72.9233	0.1748	157	0.1596	2748	2905	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	0.5056	-0.5137	0.1784	0.8888	-0.1942	0.4946	0.0302	-0.0788	-0.0319	-0.0672	0.0661	0.2591	-0.0733	-0.1394	-0	0.2631	0.0011	0.041	0.162	0.0019	0.1884	46.2456	24.0343	106.2819
2	0.5587	-0.3599	-0.2354	0.4773	0.5575	0.6376	0.0107	-0.0522	-0.093	0.0255	0.0395	-0.1532	0.0332	0.0947	0.0034	0.2137	-0.0164	0.0053	0.1815	-0.0097	0.1673	57.9962	10.0807	107.979
3	0.9036	-0.4218	-0.6432	0.2957	-0.0492	1.1027	0.047	0.0384	-0.0999	-0.0238	-0.0252	0.0885	-0.0111	-0.074	0.0006	0.203	-0.0311	0.0228	0.1523	-0.0099	0.1697	54.4347	11.5087	104.5843
4	0.4139	0.3375	-0.1416	0.57	0.1137	0.2018	0.1839	-0.1299	0.2052	0.0847	-0.1238	0.1888	-0.165	0.1483	0	0.2552	-0.0615	0.0278	0.2301	0.0004	0.2389	85.6409	33.5185	89.5055
5	0.4854	0.2585	-0.5067	0.5649	-0.1942	0.4399	0.0765	-0.1507	-0.1276	-0.0112	-0.1729	-0.0334	0.0349	0.158	-0.0064	0.1418	-0.0128	-0.0206	0.2241	0.037	0.2058	86.7829	15.4847	91.4185
6	0.5637	0.0859	-0.108	0.5582	0.0643	0.4627	0.0814	-0.1781	-0.0032	0.1153	-0.1109	0.1286	-0.0767	0.121	-0	0.1621	-0.0636	0.0099	0.2189	0.0259	0.1471	83.5664	19.1624	98.3794
7	0.0535	0.0851	0.008	0.1383	-0.0744	0.0906	-0.0452	0.6484	0.15	-0.0973	0.1022	-0.0597	-0.1634	0.3365	-0.0001	0.2565	0.0099	0.0232	0.3636	0.0478	0.2214	87.9678	21.0661	70.7076
8	0.0173	0.0193	0.0665	0.0107	0.0338	0.0937	-0.1257	0.2664	0.1153	-0.2495	0.0923	0.1125	0.1017	0.0725	-0	0.268	0.0056	-0.0679	0.3046	-0.0035	0.2807	57.7422	9.34	58.5263
9	0.0531	0.062	0.0468	0.0816	0.0844	0.1694	-0.1582	0.1243	0.4351	-0.1049	-0.03	0.078	-0.2182	0.1241	-0.0103	0.2847	0.0846	-0.0878	0.2659	0.0253	0.4178	52.5351	21.6395	64.3945
10	0.1183	0.0327	0.0086	0.4573	-0.3486	0.2428	0.013	0.0407	0.1613	0.0294	-0.0253	0.2067	0.0097	0.0271	-0.0006	0.1598	0.0251	-0.0522	0.1893	-0.0036	0.2461	56.6489	12.4173	66.1019
11	0.1053	0.028	-0.1134	0.0156	-0.0442	0.1967	0.0534	-0.0475	0.0836	0.0896	-0.0854	-0.0327	0.0591	0.004	-0	0.2067	0.0121	0.0056	0.1992	-0.0278	0.2174	67.5692	2.2146	78.17
12	0.1625	-0.0829	0.154	0.0272	-0.0747	0.2608	0.0448	-0.1453	0.1451	0.1157	-0.1587	0.4781	-0.0669	-0.2826	-0.0001	0.2128	0.0079	0.0213	0.2611	-0.1146	0.396	49.6056	13.5435	82.4025
13	0.0912	0.0738	-0.0541	0.309	-0.0591	0.1289	0.267	0.1769	-0.5556	-0.2045	-0.1447	0.5777	0.2212	0.1546	0.0412	0.2754	0.0542	-0.0697	0.261	-0.0574	0.2363	60.7637	-9.942	68.874
14	0.174	-0.0402	0.0465	0.0355	-0.0553	0.0328	0.0394	0.0393	-0.0684	0.1364	-0.0935	0.0744	0.1439	0.037	-0.0001	0.2079	0.0352	0.0037	0.2307	-0.0268	0.1858	69.14	-7.7072	73.5153
15	0.0541	0.0873	0.0386	0.1549	0.0977	0.0391	0.0615	-0.1339	-0.068	-0.0331	-0.0907	-0.1855	0.0357	0.1875	-0.0019	0.2163	0.0049	-0.034	0.1852	0.0002	0.1939	75.9184	7.9518	83.9415
16	0.0528	0.1112	0.0264	0.2344	0.0318	0.0561	0.1332	0.0958	-0.0117	0.0689	-0.1018	0.183	0.0058	0.0049	-0	0.1856	-0.0213	-0.0007	0.2114	-0.029	0.2521	59.8041	6.9407	78.1432
17	0.0275	0.0248	-0.002	0.2076	0.0631	-0.0083	0.2161	-0.0195	-0.0183	-0.065	-0.0827	-0.2667	0.1244	0.014	0	0.2311	0.0247	0.016	0.2614	-0.0495	0.3831	71.8244	1.9701	73.3412
18	0.0546	-0.0431	-0.0558	0.0383	0.0539	0.4311	-0.0172	0.1536	0.1319	-0.2984	-0.0242	-0.0629	0.0837	0.1084	0.0007	0.2528	0.0501	-0.0285	0.2327	-0.0052	0.2224	67.3474	0.6228	60.2902
19	0.0207	-0.0272	0.0246	0.0781	-0.0577	0.3032	0.1167	-0.2363	0.1399	0.0789	0.1621	0.362	0.0872	-0.4295	0.0253	0.2095	0.0067	-0.0133	0.324	-0.0198	0.528	40.7911	4.5471	77.5479
20	0.0512	0.0458	-0.0264	-0.0104	0.0114	0.0054	0.0126	-0.0561	-0.0035	-0.117	0.2453	-0.3184	-0.103	0.2163	-0.0003	0.5755	-0.0314	0.2296	0.4977	-0.1394	0.7071	67.4302	11.1218	90.9192

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 291 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 3 through 91 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 92 through 182 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 183 through 269 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 270 through 294 )	B
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3 through 23 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 24 through 38 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 39 through 91 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 92 through 114 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 115 through 139 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 140 through 164 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 165 through 181 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 182 through 198 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 199 through 220 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 221 through 242 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 243 through 270 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 271 through 292 )	C
20	X-RAY DIFFRACTION	20	(chain 'A' and resid 301) or (chain 'B' and resid 301) or (chain 'C' and resid 301)	D

-
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