PDB-4x3l: Crystal Structure of TTHA0275 from Thermus thermophilus (HB8) in ...

ID or keywords:

Entry

Database: PDB / ID: 4x3l

Title

Crystal Structure of TTHA0275 from Thermus thermophilus (HB8) in complex with 5'-methylthioadenosine in space group P21212

Components

RNA 2'-O ribose methyltransferase

Keywords

TRANSFERASE / TTHA0275 Methyltransferase AdoMet 5'-methylthioadenosine

Function / homology

Function and homology information

RNA methyltransferase activity /

RNA processing /

RNA binding /

cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Demirci, H. / Belardinelli, R. / Jogl, G.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM019756	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM094157	United States

Citation

Journal: To Be Published
Title: Crystal Structure of TTHA0275 from Thermus thermophilus (HB8)
Authors: Demirci, H. / Belardinelli, R. / Jogl, G.

History

Deposition	Dec 1, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 22, 2017	Group: Source and taxonomy
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	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	4x3l.cif.gz	225.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4x3l.ent.gz	180.1 KB	Display	PDB format
PDBx/mmJSON format	4x3l.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/x3/4x3l ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x3l	HTTPS FTP

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Related structure data

Related structure data	4x3mC 1ipaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x3m-d 5kzk-d 1x7p-d 6usc-1 2nyr-d 5l0z-d 5cyy-1 5cyy-2 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: RNA 2'-O ribose methyltransferase

B: RNA 2'-O ribose methyltransferase

hetero molecules

56.8 kDa, 2 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)	111.170, 115.950, 58.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	RNA 2'-O ribose methyltransferase Mass: 28036.334 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0275 / Plasmid: pET26b / Production host: Escherichia coli / Strain (production host): BL21 (DE3) / References: UniProt: Q5SLL8
#2: Chemical	ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 450 / 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: 3.37 Å³/Da / Density % sol: 63.53 %
Crystal grow	Temperature: 277 K / Method: microbatch / pH: 4 Details: 100 mM citric acid, and 1M Lithium chloride anyhydrous

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.7→40 Å / Num. obs: 84050 / % possible obs: 99.9 % / Redundancy: 8.95 % / R_merge(I) obs: 0.041 / Net I/σ(I): 28.61
Reflection shell	Resolution: 1.7→1.74 Å / Redundancy: 7.19 % / R_merge(I) obs: 0.629 / Mean I/σ(I) obs: 3.55 / % possible all: 99.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1IPA

1ipa

Resolution: 1.7→38.112 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2071	4183	4.98 %
R_work	0.185	79864	-
obs	0.1862	84047	99.88 %

Solvent computation

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

Displacement parameters

B_iso max: 151.32 Å² / B_iso mean: 45.0879 Å² / B_iso min: 21.19 Å²

Refinement step

Cycle: final / Resolution: 1.7→38.112 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3950	0	45	450	4445
B_iso mean	-	-	42.47	50.83	-
Num. residues	-	-	-	-	520

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4139
X-RAY DIFFRACTION	f_angle_d	0.951	5621
X-RAY DIFFRACTION	f_chiral_restr	0.041	639
X-RAY DIFFRACTION	f_plane_restr	0.005	748
X-RAY DIFFRACTION	f_dihedral_angle_d	10.936	1585

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 (%)
1.6999-1.7193	0.3417	151	0.3073	2605	2756	100
1.7193-1.7395	0.2886	142	0.2882	2622	2764	100
1.7395-1.7607	0.2677	132	0.278	2641	2773	100
1.7607-1.783	0.2688	125	0.2629	2653	2778	100
1.783-1.8064	0.2573	110	0.2522	2628	2738	100
1.8064-1.8312	0.2738	140	0.2442	2654	2794	100
1.8312-1.8573	0.241	142	0.2311	2636	2778	100
1.8573-1.8851	0.256	123	0.2433	2647	2770	100
1.8851-1.9145	0.2632	142	0.2394	2596	2738	99
1.9145-1.9459	0.2565	142	0.2297	2649	2791	100
1.9459-1.9795	0.1995	122	0.2094	2629	2751	100
1.9795-2.0155	0.2294	122	0.1987	2664	2786	100
2.0155-2.0542	0.2411	134	0.2138	2640	2774	100
2.0542-2.0961	0.2358	129	0.2048	2710	2839	100
2.0961-2.1417	0.2263	142	0.2065	2609	2751	100
2.1417-2.1915	0.2362	133	0.1955	2654	2787	100
2.1915-2.2463	0.2096	137	0.2048	2627	2764	100
2.2463-2.3071	0.2298	163	0.2014	2606	2769	99
2.3071-2.3749	0.224	145	0.1938	2660	2805	100
2.3749-2.4516	0.1916	143	0.1918	2681	2824	100
2.4516-2.5392	0.2272	132	0.1889	2649	2781	100
2.5392-2.6408	0.2424	144	0.2021	2658	2802	100
2.6408-2.761	0.2226	153	0.1996	2663	2816	100
2.761-2.9065	0.2279	129	0.2007	2673	2802	100
2.9065-3.0885	0.2324	161	0.1952	2686	2847	100
3.0885-3.3269	0.2081	157	0.1881	2656	2813	100
3.3269-3.6614	0.1865	127	0.179	2731	2858	100
3.6614-4.1907	0.1835	146	0.1566	2732	2878	100
4.1907-5.2776	0.1696	144	0.1411	2749	2893	100
5.2776-38.1217	0.1861	171	0.1718	2856	3027	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	0.0142	-0.0034	-0.0022	0.0006	0.0239	0.0271	-0.1957	0.0657	-0.2243	-0.2378	-0.1412	-0.1006	-0.1036	0.1107	-0	0.2636	-0.0621	0.0784	0.3963	0.0411	0.5427	51.4924	28.73	6.4177
2	0.026	-0.0107	-0.0186	0.0252	0.0084	0.0016	-0.214	-0.1346	-0.1958	-0.2208	-0.1399	-0.133	-0.2872	-0.131	-0	0.1496	-0.0887	0.0384	0.2899	0.1445	0.5162	43.4672	19.8052	15.2507
3	0.0067	0.0147	-0.0388	0.0471	-0.0075	0.0181	0.0778	0.1088	0.1315	0.001	-0.1671	0.0794	0.0481	0.0832	0	0.2648	-0.0763	-0.0078	0.2798	-0.0275	0.3964	33.656	29.982	11.8599
4	0.0113	0.0007	0.0049	0.0314	-0.0534	0.0435	-0.11	0.0786	0.3426	-0.0845	-0.0355	-0.2177	-0.0898	-0.0252	-0	0.3462	-0.0794	-0.0119	0.34	-0.0059	0.4434	39.439	36.9193	5.1513
5	0.0016	0.0089	-0.0069	-0.0136	0.0216	0.0074	-0.0858	0.1738	-0.0587	-0.2199	-0.1575	0.0563	0.0568	0.0288	-0	0.4083	-0.0961	0.0863	0.4135	-0.044	0.4263	44.1404	24.8596	-0.7258
6	-0.012	0.034	0.0176	-0.0174	-0.0033	-0.0064	0.1553	-0.1301	0.1191	0.0931	-0.257	-0.3398	0.1522	-0.1028	0	0.3536	-0.1772	-0.0465	0.341	0.0129	0.2859	34.6556	22.4629	21.037
7	0.0485	0.0804	0.0375	0.0207	0.0083	0.059	-0.0685	-0.1253	-0.073	-0.0033	-0.0272	-0.0652	-0.0352	0.0661	0	0.2559	-0.0284	0.0035	0.2871	0.0113	0.2135	21.7579	9.8482	18.2412
8	0.0715	0.0265	-0.0659	0.4172	0.0378	0.0937	-0.0217	-0.1159	-0.0099	-0.0969	0.0747	-0.117	0.0519	-0.0076	-0	0.2257	-0.0577	-0.0082	0.2478	0.0348	0.2386	26.57	12.9755	16.9173
9	-0.0114	-0.0066	0.037	-0.0069	0.0061	0.0128	0.1276	-0.1606	-0.4959	0.0366	0.0877	-0.0321	0.0127	-0.1658	-0	0.24	-0.075	-0.0484	0.2504	0.0458	0.1881	11.6416	0.6811	18.4028
10	0.0346	0.0426	0.0202	0.1182	-0.0137	0.0298	0.256	-0.2588	-0.2078	-0.0895	-0.1245	-0.1583	0.1029	-0.2349	0	0.2245	-0.0405	-0.0291	0.2079	0.017	0.2352	14.0257	3.3933	14.7754
11	0.0082	0.0811	0.1154	0.0658	0.0699	0.0086	0.4089	0.191	-1.0618	0.0682	0.0558	-0.2963	-0.0554	-0.1019	0	0.3	-0.1169	-0.1041	0.116	0.0516	0.3058	14.4612	-3.2771	11.7401
12	0.0049	-0.0103	0.0467	0.0204	0.0558	0.0113	-0.0648	-0.112	-0.0925	-0.013	0.0082	0.0486	-0.0609	-0.035	0	0.2466	-0.0513	-0.0273	0.1982	-0.0191	0.1445	9.3287	10.7056	10.5834
13	0.0453	0.0456	-0.0654	-0.0012	0.0491	0.0257	0.1744	-0.0555	0.1777	-0.3038	-0.307	-0.5032	0.0199	-0.2621	-0	-0.045	0.2631	0.2259	0.2127	0.2679	0.6962	38.8997	-6.0404	-18.6535
14	0.0733	-0.084	-0.1068	0.1701	-0.12	0.0077	0.0982	-0.1523	0.0693	-0.2089	-0.1387	-0.1854	0.1112	-0.0118	-0	0.2902	0.0362	-0.0468	0.2698	0.0752	0.4618	33.1407	-13.2528	-10.6502
15	0.0152	0.0191	0.0017	0.0073	0.0016	-0.0059	-0.0526	0.0857	-0.0554	-0.1634	-0.0843	-0.2106	0.0701	-0.0742	-0	0.4026	-0.0014	0.0154	0.3149	0.056	0.3203	22.4775	-4.5838	-20.5538
16	0.0187	-0.0355	-0.086	0.0838	0.0393	0.0431	-0.1029	0.1443	-0.1257	-0.078	-0.0947	-0.1601	-0.0369	-0.0908	-0	0.2582	-0.0599	-0.011	0.289	0.0471	0.212	13.0359	9.1818	-12.2014
17	0.2407	0.0525	-0.0848	0.4558	0.3018	0.1703	-0.0291	0.067	0.033	0.0044	-0.0345	-0.0931	0.0437	-0.0446	-0	0.2657	-0.0178	-0.0209	0.2769	0.0402	0.2058	15.095	8.442	-12.2691
18	0.018	-0.0792	-0.0281	0.1086	0.0106	0.0442	0.048	-0.044	0.0294	0.0101	-0.1654	-0.0569	-0.1436	-0.0597	0	0.2474	-0.0535	-0.0189	0.2494	0.0175	0.2491	9.2694	16.2719	-5.3595
19	-0.0005	0.0716	-0.0788	0.1037	0.0222	0.0492	0.5626	-0.1412	0.319	-0.2333	0.0373	-0.2464	-0.3923	0.0095	-0	0.3856	0.026	0.0031	0.19	0.0078	0.2967	11.8496	22.7535	-3.4455
20	0.0248	0.045	-0.0123	0.0409	0.015	0.0092	-0.0707	0.0143	0.2741	-0.0432	0.0967	0.0958	0.136	0.0092	-0	0.2479	-0.0375	-0.0296	0.2117	0.0035	0.1618	6.3994	9.3453	0.912

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 18 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 33 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 52 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 53 through 73 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 74 through 88 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 89 through 102 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 103 through 121 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 122 through 178 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 179 through 193 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 194 through 215 )	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 216 through 238 )	A
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 239 through 260 )	A
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 33 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 34 through 88 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 89 through 102 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 103 through 121 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 122 through 193 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 194 through 215 )	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 216 through 238 )	B
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 239 through 260 )	B

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