PDB-3t94: Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylas...

ID or keywords:

Entry

Database: PDB / ID: 3t94

Title

Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) II complexed with 5'-deoxy-5'-methylthioadenosine and sulfate

Components

5'-methylthioadenosine phosphorylase (MtaP)

Keywords

TRANSFERASE / ALPHA/BETA /

BETA BARREL /

nucleoside phosphorylase

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 /

cytosol
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.452 Å

Authors

Zhang, Y. / Ealick, S.E.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II.
Authors: Zhang, Y. / Zwart, P.H. / Ealick, S.E.

History

Deposition	Aug 2, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 24, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 29, 2012	Group: Database references
Revision 1.2	Mar 28, 2012	Group: Database references
Revision 1.3	Sep 13, 2023	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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3t94.cif.gz	686.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3t94.ent.gz	569.7 KB	Display	PDB format
PDBx/mmJSON format	3t94.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t9/3t94 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/3t94	HTTPS FTP

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Related structure data

Related structure data	1cg6S 2a8y S: Starting model for refinement
Similar structure data	2a8y-2 2a8y-1 1wta-2 4xis-1 6qru-1 6qrr-1 4us6-1 4qe4-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: 5'-methylthioadenosine phosphorylase (MtaP)

B: 5'-methylthioadenosine phosphorylase (MtaP)

C: 5'-methylthioadenosine phosphorylase (MtaP)

D: 5'-methylthioadenosine phosphorylase (MtaP)

E: 5'-methylthioadenosine phosphorylase (MtaP)

F: 5'-methylthioadenosine phosphorylase (MtaP)

hetero molecules

184 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 5'-methylthioadenosine phosphorylase (MtaP)

B: 5'-methylthioadenosine phosphorylase (MtaP)

C: 5'-methylthioadenosine phosphorylase (MtaP)

hetero molecules

A: 5'-methylthioadenosine phosphorylase (MtaP)

B: 5'-methylthioadenosine phosphorylase (MtaP)

C: 5'-methylthioadenosine phosphorylase (MtaP)

hetero molecules

defined by author&software
184 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: 5'-methylthioadenosine phosphorylase (MtaP)

E: 5'-methylthioadenosine phosphorylase (MtaP)

F: 5'-methylthioadenosine phosphorylase (MtaP)

hetero molecules

D: 5'-methylthioadenosine phosphorylase (MtaP)

E: 5'-methylthioadenosine phosphorylase (MtaP)

F: 5'-methylthioadenosine phosphorylase (MtaP)

hetero molecules

defined by author&software
184 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.160, 138.093, 96.560
Angle α, β, γ (deg.)	90.00, 92.21, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	5'-methylthioadenosine phosphorylase (MtaP) Mass: 30177.795 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PET-22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q97W94, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical	ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine Mass: 297.334 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1275 / 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: 2.49 Å³/Da / Density % sol: 50.53 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: AMMONIUM SULFATE, BIS-TRIS, PH 6.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97946 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2004
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.45→40 Å / Num. all: 301528 / Num. obs: 301528 / % possible obs: 97.2 % / B_iso Wilson estimate: 12.46 Å²
Reflection shell	Resolution: 1.45→1.53 Å / Num. unique all: 42086 / % possible all: 93

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Processing

Software

Name	Version	Classification
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection
HKL-2000		data reduction
SCALA		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1CG6

1cg6

Resolution: 1.452→39.668 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8155 / SU ML: 0.32 / σ(F): 0 / Phase error: 24.8 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1853	20904	6.93 %	RANDOM
R_work	0.1687	-	-	-
all	0.17	301528	-	-
obs	0.17	301431	97.09 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.816 Å² / k_sol: 0.365 e/Å³

Displacement parameters

B_iso max: 99.18 Å² / B_iso mean: 28.7796 Å² / B_iso min: 15.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-9.5609 Å²	-0 Å²	-0.9584 Å²
2-	-	-9.2642 Å²	-0 Å²
3-	-	-	-10.164 Å²

Refinement step

Cycle: LAST / Resolution: 1.452→39.668 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12292	0	175	1275	13742

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	13878
X-RAY DIFFRACTION	f_angle_d	1.198	18926
X-RAY DIFFRACTION	f_chiral_restr	0.072	2144
X-RAY DIFFRACTION	f_plane_restr	0.005	2409
X-RAY DIFFRACTION	f_dihedral_angle_d	12.755	5080

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 (%)
1.452-1.4685	0.2524	476	0.2307	8641	9117	88
1.4685-1.4858	0.2409	525	0.214	9261	9786	94
1.4858-1.5039	0.236	491	0.2009	9214	9705	95
1.5039-1.523	0.2288	511	0.1924	9243	9754	95
1.523-1.543	0.2163	545	0.1833	9246	9791	95
1.543-1.5641	0.1919	504	0.1786	9411	9915	95
1.5641-1.5865	0.1986	503	0.1752	9429	9932	96
1.5865-1.6102	0.2013	500	0.1764	9467	9967	96
1.6102-1.6353	0.2003	489	0.1722	9415	9904	96
1.6353-1.6621	0.1982	510	0.1708	9449	9959	96
1.6621-1.6908	0.1988	481	0.1704	9436	9917	96
1.6908-1.7215	0.2176	458	0.1728	9522	9980	97
1.7215-1.7546	0.187	536	0.1682	9532	10068	97
1.7546-1.7905	0.1786	578	0.1683	9445	10023	97
1.7905-1.8294	0.1728	801	0.1631	9246	10047	98
1.8294-1.872	0.1806	805	0.1613	9274	10079	98
1.872-1.9188	0.18	842	0.1632	9255	10097	98
1.9188-1.9706	0.1802	909	0.1671	9276	10185	98
1.9706-2.0286	0.1863	874	0.1673	9256	10130	98
2.0286-2.0941	0.1885	897	0.1751	9328	10225	98
2.0941-2.1689	0.1743	857	0.1663	9273	10130	98
2.1689-2.2558	0.1895	858	0.1664	9389	10247	99
2.2558-2.3584	0.1927	912	0.1639	9342	10254	99
2.3584-2.4828	0.1866	852	0.1695	9434	10286	99
2.4828-2.6383	0.1975	884	0.1719	9342	10226	99
2.6383-2.8419	0.1879	822	0.1737	9474	10296	99
2.8419-3.1278	0.1853	875	0.1732	9460	10335	99
3.1278-3.5802	0.1871	918	0.1611	9452	10370	100
3.5802-4.5096	0.1516	909	0.1392	9413	10322	99
4.5096-39.6831	0.1909	782	0.1797	9602	10384	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	0.0728	0.0871	-0.0134	0.4748	-0.2781	0.1037	0.05	-0.3223	-0.0565	0.2427	-0.0432	-0.1892	0.0273	-0.0128	-0	0.2813	-0.04	-0.0019	0.3008	0.0311	0.3086	-15.6143	-23.5733	8.3567
2	1.2365	0.1795	0.3077	0.7019	-0.1779	0.929	0.0287	-0.1097	-0.1177	0.0361	-0.002	0.0132	0.0868	-0.0827	-0	0.184	-0.0216	0.0168	0.2151	0.0148	0.1739	-18.2182	-16.2935	2.6045
3	0.6587	0.0953	0.0044	0.2988	-0.0884	0.4341	-0.0265	0.0172	-0.1096	-0.0439	0.026	0.0513	0.0969	-0.0824	0	0.1956	-0.0287	0.0073	0.2256	0.0076	0.1878	-24.0197	-14.8185	-7.0951
4	0.9529	0.6906	0.4069	1.0752	-0.4832	0.8161	0.0582	0.072	-0.0137	-0.0738	0.0243	-0.0367	0.0823	-0.1797	-0.0001	0.252	-0.0569	0.0215	0.3132	0.0373	0.2458	-30.1696	-17.3326	2.0921
5	0.0185	-0.0231	0.0056	0.0319	0.0095	0.0207	0.0271	-0.0009	-0.2405	-0.0425	0.1342	-0.0655	0.194	0.0858	0.0004	0.3769	-0.0228	0.0202	0.3193	-0.0572	0.3703	-6.0145	-23.5521	-17.343
6	0.1224	-0.1267	-0.0207	0.3286	0.3435	0.2901	-0.1404	-0.1337	0.2842	0.085	0.059	-0.2678	-0.3131	0.1701	-0.0002	0.2845	0.0535	-0.0158	0.3228	-0.0449	0.2779	-13.3959	25.7857	6.0023
7	0.7674	-0.133	0.3477	0.5162	-0.1502	0.69	-0.0387	-0.0339	0.1037	0.0108	0.0086	0.0104	-0.0885	-0.0518	-0.0001	0.1707	0.0245	0.0118	0.196	-0.0124	0.1558	-16.4062	17.4189	-1.5618
8	0.9405	-0.3375	0.2487	0.8505	0.2168	0.9332	0.0038	0.037	0.0719	-0.0721	-0.0493	0.0612	-0.1126	-0.0637	0.0001	0.1865	0.0249	0.0075	0.2096	0.0011	0.178	-22.6932	18.0117	-12.0883
9	0.6853	-0.1561	0.4655	0.5205	0.3216	0.538	-0.2337	-0.1968	-0.5105	0.1336	-0.0321	0.0925	0.3329	-0.076	-0.0005	0.2829	0.0729	0.071	0.3215	-0.0362	0.3808	-26.7843	27.4381	1.0283
10	0.023	0.0128	-0.0057	0.009	0.0142	0.0369	-0.0483	-0.2181	-0.0317	0.2218	-0.0032	0.0764	-0.0401	-0.1597	-0.0001	0.2876	0.0274	0.0985	0.458	-0.0052	0.3242	-27.3276	2.6865	11.6044
11	0.3147	0.2086	-0.2378	0.057	-0.0575	0.3916	-0.0302	0.176	-0.2914	0.0115	0.1084	-0.3753	0.0533	0.5412	0.0158	0.2685	-0.0224	0.0315	0.4277	-0.0208	0.2365	10.8881	-2.0147	-27.6233
12	0.7976	-0.0987	0.194	0.601	0.2845	0.983	0.0297	0.1124	-0.0395	-0.0638	-0.0192	-0.0082	0.0049	0.0842	-0	0.1667	0.003	0.0177	0.2319	-0.0026	0.1383	0.382	-1.2757	-23.8212
13	1.0057	-0.004	-0.1951	0.527	-0.0832	1.3893	0.0094	0.1512	-0.0758	-0.0787	-0.0191	0.0346	0.0795	-0.1351	-0.0001	0.179	0.0055	0.0086	0.2512	-0.019	0.147	-10.5562	-5.8521	-28.8917
14	0.7252	0.0679	0.2574	0.1348	-0.0393	0.6498	0.0376	0.0508	0.2109	0.3751	-0.0483	0.1661	-0.5522	-0.142	-0.0003	0.4086	0.0538	0.0566	0.4075	0.033	0.2012	2.2077	0.6021	-38.3409
15	0.0311	-0.0031	-0.0236	0.0317	-0.0318	0.0352	0.081	0.3891	0.1911	-0.0767	0.0834	-0.2321	-0.1972	0.2614	-0.0005	0.3949	-0.0148	0.0699	0.3535	0.0426	0.2793	-3.2848	20.7524	-21.3016
16	0.1208	0.0394	-0.0014	0.4532	-0.3495	0.12	0.153	-0.3649	-0.1121	0.1438	-0.0567	-0.0679	-0.0211	0.0028	0	0.2494	-0.043	-0.0136	0.2226	0.0379	0.3501	54.4166	-20.5799	-39.8018
17	0.9846	0.139	0.1522	0.7761	-0.0776	0.5593	0.0286	-0.0703	-0.0857	0.0304	0.006	0.0993	0.075	-0.0546	0	0.1704	-0.0174	-0.0127	0.134	0.0154	0.2197	52.6352	-12.8759	-47.5256
18	0.5747	0.4009	0.0938	1.2866	-0.3113	0.6329	-0.0206	-0.0205	0.0304	-0.0651	0.0853	0.289	0.0476	-0.1125	-0.0001	0.1729	-0.0261	-0.0239	0.1635	0.022	0.284	40.6259	-8.3617	-52.6883
19	0.5697	0.0663	0.3449	0.5707	-0.1549	0.4864	0.023	0.3302	0.0344	-0.5916	0.2423	-0.2747	-0.1707	0.3564	0.008	0.3734	-0.1343	-0.022	0.2514	0.0003	0.4197	43.907	-25.262	-48.5676
20	0.0179	-0.0235	0.0106	0.0333	0.0087	0.026	0.019	-0.0454	-0.3668	-0.0076	0.0664	-0.0135	0.2311	0.0288	0.0003	0.4033	-0.032	-0.008	0.2433	-0.0456	0.3867	63.3455	-20.0029	-65.5991
21	0.1939	-0.1383	-0.0635	0.3695	0.3752	0.3097	-0.1404	-0.0813	0.2437	0.0627	0.0413	-0.1951	-0.1745	0.263	-0.0001	0.2576	0.0411	-0.036	0.2353	-0.0265	0.3011	55.9241	29.186	-42.1755
22	1.007	-0.1251	0.493	0.7935	-0.018	0.7222	-0.0597	-0.0569	0.0846	0.0549	0.021	0.0263	-0.0672	-0.0295	0	0.1757	0.0063	-0.0134	0.1417	-0.0056	0.2013	54.1224	23.9313	-49.0202
23	0.2973	-0.0795	0.1678	0.6448	-0.0967	0.4826	-0.0112	-0.0159	-0.0076	-0.0008	-0.0055	0.1706	-0.0449	-0.0648	-0.0001	0.1576	0.0094	-0.0182	0.144	-0.0095	0.2209	45.3331	18.0487	-55.4611
24	1.2776	-0.7036	0.4903	1.3792	0.6539	0.7914	-0.131	0.0184	0.0644	-0.0852	0.0119	0.2327	0.1132	-0.1146	-0.0009	0.2286	0.0071	-0.0258	0.1679	-0.0074	0.3216	47.8326	29.4498	-57.5011
25	0.0212	0.009	-0.0019	0.0024	0.01	0.046	-0.1569	-0.2218	0.0742	0.1908	-0.0877	0.0289	-0.1232	-0.1342	0.0004	0.3217	0.0356	0.1095	0.3184	-0.0028	0.3887	42.1462	6.2394	-36.6185
26	0.2927	0.0712	-0.2703	0.018	-0.0699	0.3292	0.0348	0.0095	-0.249	-0.0315	-0.0281	-0.316	0.1579	0.3875	0.0007	0.3373	-0.0038	0.0242	0.3298	-0.0061	0.2623	80.1318	1.3986	-75.9424
27	0.6174	-0.024	0.2102	0.6724	0.1425	0.8032	0.0024	0.1036	-0.033	-0.1434	0.0072	-0.0301	0.0481	0.0724	0	0.2169	-0.0018	0.0029	0.1772	-0.0092	0.1757	70.4668	2.5157	-71.7983
28	0.8561	0.0942	-0.1024	0.7699	-0.242	1.2487	-0.0051	0.1434	-0.0785	-0.2194	0.0193	0.0465	0.1307	-0.0678	0.0001	0.2585	-0.004	-0.0257	0.1816	-0.0142	0.1813	59.4827	-2.4132	-77.4048
29	0.7296	0.1007	0.1848	0.0926	0.0027	0.5215	0.0958	-0.0941	0.2349	0.3223	-0.0876	0.2513	-0.5107	-0.0896	0	0.5289	0.0292	0.04	0.334	0.0217	0.2459	71.6073	4.223	-86.6215
30	0.0269	0.0041	-0.0073	0.03	-0.0252	0.0142	0.1206	0.2769	0.2188	-0.0696	0.188	-0.2289	-0.192	0.2039	-0.0016	0.3707	-0.0393	0.0223	0.3004	0.032	0.3282	66.1435	24.2717	-69.4668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 1:23)	A	1 - 23
2	X-RAY DIFFRACTION	2	(chain A and resid 24:120)	A	24 - 120
3	X-RAY DIFFRACTION	3	(chain A and resid 121:214)	A	121 - 214
4	X-RAY DIFFRACTION	4	(chain A and resid 215:263)	A	215 - 263
5	X-RAY DIFFRACTION	5	(chain A and resid 264:270)	A	264 - 270
6	X-RAY DIFFRACTION	6	(chain B and resid 1:23)	B	1 - 23
7	X-RAY DIFFRACTION	7	(chain B and resid 24:134)	B	24 - 134
8	X-RAY DIFFRACTION	8	(chain B and resid 135:234)	B	135 - 234
9	X-RAY DIFFRACTION	9	(chain B and resid 235:263)	B	235 - 263
10	X-RAY DIFFRACTION	10	(chain B and resid 264:270)	B	264 - 270
11	X-RAY DIFFRACTION	11	(chain C and resid 1:23)	C	1 - 23
12	X-RAY DIFFRACTION	12	(chain C and resid 24:134)	C	24 - 134
13	X-RAY DIFFRACTION	13	(chain C and resid 135:234)	C	135 - 234
14	X-RAY DIFFRACTION	14	(chain C and resid 235:263)	C	235 - 263
15	X-RAY DIFFRACTION	15	(chain C and resid 264:270)	C	264 - 270
16	X-RAY DIFFRACTION	16	(chain D and resid 1:23)	D	1 - 23
17	X-RAY DIFFRACTION	17	(chain D and resid 24:134)	D	24 - 134
18	X-RAY DIFFRACTION	18	(chain D and resid 135:235)	D	135 - 235
19	X-RAY DIFFRACTION	19	(chain D and resid 236:263)	D	236 - 263
20	X-RAY DIFFRACTION	20	(chain D and resid 264:270)	D	264 - 270
21	X-RAY DIFFRACTION	21	(chain E and resid 1:23)	E	1 - 23
22	X-RAY DIFFRACTION	22	(chain E and resid 24:120)	E	24 - 120
23	X-RAY DIFFRACTION	23	(chain E and resid 121:214)	E	121 - 214
24	X-RAY DIFFRACTION	24	(chain E and resid 215:263)	E	215 - 263
25	X-RAY DIFFRACTION	25	(chain E and resid 264:270)	E	264 - 270
26	X-RAY DIFFRACTION	26	(chain F and resid 1:23)	F	1 - 23
27	X-RAY DIFFRACTION	27	(chain F and resid 24:134)	F	24 - 134
28	X-RAY DIFFRACTION	28	(chain F and resid 135:234)	F	135 - 234
29	X-RAY DIFFRACTION	29	(chain F and resid 235:263)	F	235 - 263
30	X-RAY DIFFRACTION	30	(chain F and resid 264:270)	F	264 - 270

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