PDB-4q37: Crystal structure of the hypothetical protein TM0182 Thermotoga m...

ID or keywords:

Entry

Database: PDB / ID: 4q37

Title

Crystal structure of the hypothetical protein TM0182 Thermotoga maritima, N-terminal domain.

Components

Radical SAM protein

Keywords

UNKNOWN FUNCTION / Alpha-beta fold

Function / homology

Function and homology information

cobalamin binding /

catalytic activity / 4 iron, 4 sulfur cluster binding / identical protein binding /

metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.19 Å

Authors

Hocker, B. / Farias-Rico, J.A.

Citation

Journal: Nat.Chem.Biol. / Year: 2014
Title: Evolutionary relationship of two ancient protein superfolds.
Authors: Farias-Rico, J.A. / Schmidt, S. / Hocker, B.

History

Deposition	Apr 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Aug 27, 2014	Group: Database references
Revision 1.2	Sep 3, 2014	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4q37.cif.gz	280.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4q37.ent.gz	231.2 KB	Display	PDB format
PDBx/mmJSON format	4q37.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/q3/4q37 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q37	HTTPS FTP

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Related structure data

Similar structure data	1dxm-d 3lyu-3 1a3a-1 3zxn-d 4q53-d 3rlo-d 3c01-1 3lyu-4 6td9-1 3lrx-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Radical SAM protein

B: Radical SAM protein

C: Radical SAM protein

D: Radical SAM protein

E: Radical SAM protein

F: Radical SAM protein

hetero molecules

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

1

A: Radical SAM protein

E: Radical SAM protein

hetero molecules

defined by author&software
30.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Radical SAM protein

defined by author&software
30 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Radical SAM protein

defined by author&software
30 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Radical SAM protein

F: Radical SAM protein

hetero molecules

defined by author&software
30.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.050, 145.300, 141.710
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Radical SAM protein / Mass: 14978.198 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0182, THEMA_03865, Tmari_0180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY26
#2: Chemical	ChemComp-PT / PLATINUM (II) ION Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.92 Å³/Da / Density % sol: 57.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 1.2 M Ammonium sulfate and 0.3 M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.0698 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2010

Radiation

Monochromator: double-crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0698 Å / Relative weight: 1

Reflection

Resolution: 3.19→39.6 Å / Num. obs: 33708 / % possible obs: 99.08 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / B_iso Wilson estimate: 67.8 Å² / R_merge(I) obs: 0.014 / R_sym value: 0.015 / Net I/σ(I): 15.01

Reflection shell

Resolution (Å)	Diffraction-ID	% possible all
3.19-3.26	1	88.5
3.27-3.35	1	99.9
3.36-3.45	1	100
3.46-3.55	1	100
3.56-3.67	1	100
3.68-3.8	1	100
3.81-3.94	1	100
3.95-4.1	1	100
4.11-4.29	1	100
4.3-4.5	1	100

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Processing

Software

Name	Version	Classification
XDS		data scaling
SHELX		model building
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XDS		data reduction
XSCALE		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.19→39.6 Å / SU ML: 0.42 / σ(F): 1.46 / Phase error: 28.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28	1676	4.97 %	RANDOM
R_work	0.2353	-	-	-
obs	0.2375	33701	99.12 %	-
all	-	33708	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.19→39.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5253	0	2	17	5272

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5387
X-RAY DIFFRACTION	f_angle_d	0.936	7337
X-RAY DIFFRACTION	f_dihedral_angle_d	12.399	1801
X-RAY DIFFRACTION	f_chiral_restr	0.035	832
X-RAY DIFFRACTION	f_plane_restr	0.004	943

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 (%)
3.19-3.2807	0.366	128	0.3428	2450	X-RAY DIFFRACTION	90
3.2807-3.3865	0.3086	139	0.302	2671	X-RAY DIFFRACTION	100
3.3865-3.5075	0.3181	137	0.2854	2682	X-RAY DIFFRACTION	100
3.5075-3.6478	0.3726	141	0.2709	2680	X-RAY DIFFRACTION	100
3.6478-3.8137	0.2683	145	0.2353	2705	X-RAY DIFFRACTION	100
3.8137-4.0146	0.2644	143	0.2341	2704	X-RAY DIFFRACTION	100
4.0146-4.2659	0.3164	137	0.2328	2679	X-RAY DIFFRACTION	100
4.2659-4.5948	0.2455	140	0.214	2680	X-RAY DIFFRACTION	100
4.5948-5.0563	0.2515	140	0.1925	2710	X-RAY DIFFRACTION	100
5.0563-5.7861	0.3383	140	0.2479	2694	X-RAY DIFFRACTION	100
5.7861-7.2824	0.2475	143	0.255	2683	X-RAY DIFFRACTION	100
7.2824-39.6048	0.2307	143	0.1876	2687	X-RAY DIFFRACTION	100

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	2.6091	1.6012	-1.5386	1.4977	-1.5575	2.7373	0.2527	-0.1957	0.3697	0.2558	-0.0345	-0.0109	-0.454	0.3298	-0.2393	0.4888	0.0261	0.0327	0.4747	-0.1467	0.3351	44.6246	23.4241	-9.5041
2	5.5638	-0.4635	0.3826	3.8558	-0.824	6.1783	-0.0107	-0.226	-0.1449	0.1588	0.0321	0.3367	-0.4001	-0.5324	0.0027	0.3753	0.0934	0.0559	0.3455	0.0176	0.3346	32.0645	20.7019	-6.1502
3	1.6545	-0.8993	1.3638	4.3801	-2.3123	2.6856	0.2197	-0.4701	-0.0676	0.073	-0.0987	-0.0956	0.0226	0.3297	-0.7175	0.7375	0.113	0.1324	0.7582	-0.0202	0.0769	59.1907	14.4106	42.5467
4	1.6173	3.2186	-1.1796	9.3413	-1.9946	3.4097	-0.592	0.169	-0.5835	-1.1207	0.3173	0.1344	-0.3454	0.6381	0.1262	0.7277	-0.1692	-0.1398	0.8045	0.1617	0.8214	51.2467	9.6406	24.7808
5	2.5446	0.3564	-2.4906	1.2101	-1.3738	3.3367	-0.122	0.6215	0.7853	-0.6464	0.5523	0.2032	-0.2071	0.0018	0.1679	0.9184	-0.4572	-0.0904	0.643	0.0776	0.4673	49.5404	20.4239	19.7003
6	1.8814	1.4422	-1.1039	2.4829	-3.3878	5.3311	-0.3235	0.0481	0.4701	0.4185	0.3194	1.9999	-2.077	-0.8579	0.0174	0.928	0.3046	-0.0965	0.517	-0.009	0.7081	34.8635	19.665	27.6736
7	9.1038	0.3428	-2.062	3.699	0.2298	4.4498	-0.0052	-1.9818	-0.2927	0.4187	0.3878	0.2813	0.0311	0.738	0.211	0.5184	-0.1063	0.0066	0.7152	0.1339	0.4212	42.2744	5.4296	31.2658
8	7.2579	0.4561	-1.401	4.2965	0.4577	3.9556	0.2305	-0.8254	0.506	-0.1091	0.0073	0.1886	0.2002	-0.1478	-0.0115	0.4511	-0.0791	0.0853	0.3087	0.0528	0.438	36.0983	5.8032	28.5431
9	3.8483	-1.9376	-1.6207	1.2799	0.3011	1.8003	-0.0476	-0.5496	0.3859	0.0319	-0.0241	0.2875	-0.0463	0.6166	-0.2959	0.5772	-0.0861	0.0302	0.3137	0.1464	0.3781	39.7784	1.6723	21.8325
10	1.1104	-0.0745	-0.8226	0.0068	0.0983	1.8087	0.0703	0.0921	0.1692	-0.6131	-0.0726	-0.0897	0.0745	0.0482	-1.6031	0.7182	-0.1458	0.0866	0.4719	0.4016	0.5421	47.4351	10.2302	14.3182
11	5.5999	5.9684	-2.7685	9.7772	-4.258	3.8368	-0.4225	0.7659	-0.038	-1.2366	0.0822	-0.6543	1.2994	0.2862	0.5684	0.7	0.0752	0.0427	0.5835	0.19	0.317	41.7939	3.2191	14.093
12	2.7297	0.9661	-1.8833	1.7581	-1.5406	3.351	0.5014	0.2358	-0.1094	0.6797	0.0265	0.2571	-0.3196	-0.8668	-0.0899	0.4167	-0.1137	-0.0371	0.7883	0.0235	0.3619	-6.2031	49.2252	33.6705
13	4.3768	1.4526	2.1219	5.711	3.1335	2.1586	0.3651	0.2239	-0.6962	-0.9776	0.5387	-0.3932	0.2497	0.5252	-0.6933	0.6165	-0.0011	-0.0462	0.613	-0.1349	0.5092	10.9427	41.0103	24.0534
14	4.5265	-0.286	0.8597	6.956	1.6989	1.6513	0.7109	-1.0287	-0.758	1.04	0.2878	-1.1673	0.8262	1.9309	-0.6514	0.6119	0.0037	-0.2533	0.9298	-0.0168	0.5445	17.7174	43.1867	40.8759
15	2.1256	-0.9133	0.056	6.6497	3.463	3.954	-0.3187	0.066	-0.2778	-0.2312	0.5283	-0.1678	-0.1003	0.3213	-0.0274	0.3613	0.0482	0.023	0.4976	-0.0679	0.3049	15.938	57.3113	35.9954
16	2.0717	-1.0212	0.0049	2.5044	-2.2997	2.6285	0.7201	0.545	-0.2568	-1.4219	-0.227	-0.2486	-0.1543	0.0494	1.1174	0.7451	0.0556	0.0867	0.9127	-0.3363	0.503	15.9026	54.9079	21.7254
17	4.6582	-0.546	-0.5731	0.628	1.0298	2.8227	-0.0687	-0.4887	1.0059	0.2162	0.0984	-0.2589	0.131	0.9287	0.0882	0.5817	0.2944	0.0233	0.7239	0.0474	0.4095	7.1085	46.7858	-0.9844
18	7.8522	2.107	-3.6662	3.8463	-1.7799	1.9028	0.4498	0.8427	1.8429	-0.2961	0.3169	-1.1037	-0.2988	-0.4332	-0.5588	0.638	0.0215	0.1676	0.3962	0.1079	1.141	15.2853	61.2671	-2.5486
19	7.9594	0.3525	0.9673	6.9257	1.2424	3.9338	-0.2908	0.2494	0.3285	-1.5672	-0.245	-0.2853	-0.4765	-0.1648	0.6593	0.6613	0.0138	0.2458	0.3699	-0.0393	1.1145	23.7463	55.9291	-7.2924
20	2.1276	-0.8792	-2.5471	6.9628	-0.986	3.6989	-0.2034	-1.1349	0.9556	-0.1329	0.102	-0.7037	0.1317	0.8571	-0.3667	0.4449	0.0661	0.0183	0.7334	-0.3239	0.5501	23.0737	46.3779	3.337
21	2.3695	1.5209	0.5702	2.8205	1.9866	1.5709	0.2594	-0.0557	0.0513	-0.5809	-0.0374	0.0129	0.3874	0.0181	0.0857	0.4268	0.2288	0.0059	0.6389	-0.1515	0.2291	41.9648	25.1604	-15.7943
22	1.3322	0.3585	-0.1716	0.6617	-1.4956	3.9964	-0.023	0.953	0.3639	-0.1468	0.2661	0.0756	-0.4137	-0.46	-0.1863	1.7943	-0.0662	0.0956	0.8954	0.1561	0.3797	49.0658	34.5793	-30.3926
23	1.0532	-1.9952	2.1089	6.5157	-5.4345	4.9836	0.061	1.5072	1.2455	-0.2001	-0.0025	-0.938	-1.3232	1.2715	0.6499	1.1939	-0.1763	0.1998	0.8709	0.3361	0.732	55.6089	38.1714	-28.2148
24	6.6255	-4.746	-3.6575	9.5024	0.0297	3.6149	-0.4662	-2.1979	0.4104	1.5794	0.3787	-1.7564	-0.4743	1.61	0.1555	0.8338	0.0776	-0.1357	1.1385	0.1746	0.9614	54.5569	39.1637	-11.082
25	4.8376	-2.7375	-3.0404	6.7705	-1.9418	4.7128	-0.5443	-0.9842	0.7217	0.645	0.5829	-0.343	-0.3645	0.739	0.1045	0.7046	-0.0026	0.0022	0.6251	-0.1993	0.6454	50.3498	43.9086	-16.9735
26	2.7309	-0.7021	0.9227	1.1912	-2.5972	6.0451	0.1711	-0.2635	-0.4587	1.6053	0.4624	0.8152	2.2991	-0.4041	0.268	1.1737	-0.2656	0.2576	0.8549	-0.4715	1.4961	34.5289	38.9063	-10.2352
27	4.4952	-0.6956	1.8771	4.2083	-1.7938	3.7753	0.461	-1.0727	0.8904	0.1026	0.0778	-0.3079	-1.1708	-0.4671	-0.1732	0.6743	0.0826	0.2159	0.5546	-0.0833	0.8973	43.0348	45.9332	-11.996
28	4.042	-1.9327	2.227	4.4275	-1.7667	3.0142	0.7177	-0.4193	0.3252	-0.0707	-0.8653	0.0136	-0.912	-0.0786	-0.415	0.5773	-0.0503	0.2816	0.6484	-0.1898	0.8902	42.1192	48.8385	-20.883
29	0.2531	0.0329	-0.0494	0.0187	0.0762	2.0371	0.3878	0.6158	0.0422	-0.5771	-0.3537	-0.0497	0.2619	0.4512	-0.0914	0.7838	0.3364	0.1003	0.6342	0.0564	0.2507	7.1346	48.3073	-18.2645
30	6.1081	-0.6792	-2.001	4.0573	0.0691	3.57	-0.1516	-1.2334	-0.629	0.5647	0.7659	0.3058	0.4036	-0.4273	-0.563	0.597	0.2729	0.0858	0.9424	0.3054	0.5606	8.4316	31.7811	-11.9473
31	6.4158	-0.7791	1.408	4.7821	-0.6601	5.6945	0.4329	0.6372	-0.2194	-0.5975	-0.2658	0.2721	0.0088	0.0951	-0.1861	0.8121	0.3674	-0.016	0.7744	-0.0098	0.3886	13.9356	33.44	-24.246

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 120 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 10 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 11 through 15 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 16 through 35 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 36 through 47 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 48 through 57 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 58 through 85 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 86 through 102 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 103 through 111 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 112 through 120 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 14 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 15 through 34 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 35 through 44 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 45 through 102 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 103 through 120 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 34 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 35 through 51 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 52 through 78 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 79 through 120 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 1 through 14 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 15 through 23 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 24 through 33 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 34 through 43 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 44 through 52 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 53 through 57 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 58 through 85 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 86 through 111 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 1 through 35 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 36 through 71 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 72 through 120 )

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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

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+About Yorodumi

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-Aug 12, 2020. Covid-19 info

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Download

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Validation report

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi