PDB-4cne: Crystal structure of E.coli TrmJ in complex with S-adenosyl-L- ho...

ID or keywords:

Entry

Database: PDB / ID: 4cne

Title

Crystal structure of E.coli TrmJ in complex with S-adenosyl-L- homocysteine

Components

TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRMJ

Keywords

TRANSFERASE / SPOUT

Function / homology

Function and homology information

tRNA (cytidine32/uridine32-2'-O)-methyltransferase / tRNA nucleoside ribose methylation / tRNA (uracil-2'-O-)-methyltransferase activity / protein homodimerization activity / RNA binding / cytosol
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Van Laer, B. / Somme, J. / Roovers, M. / Steyaert, J. / Droogmans, L. / Versees, W.

Citation

Journal: RNA / Year: 2014
Title: Characterization of Two Homologous 2'-O-Methyltransferases Showing Different Specificities for Their tRNA Substrates.
Authors: Somme, J. / Van Laer, B. / Roovers, M. / Steyaert, J. / Versees, W. / Droogmans, L.

History

Deposition	Jan 22, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 30, 2014	Group: Database references
Revision 1.2	Sep 13, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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	4cne.cif.gz	145.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4cne.ent.gz	113.1 KB	Display	PDB format
PDBx/mmJSON format	4cne.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4cne_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4cne_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4cne_validation.xml.gz	15.1 KB	Display
Data in CIF	4cne_validation.cif.gz	19.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cn/4cne ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cne	HTTPS FTP

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Related structure data

Related structure data	4cndSC 4cnfC 4cngC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vus-16 2vut-14 2vut-13 2vus-13 1gqz-d 2vut-9 6ovp-d 3dpk-d 5nxk-1 2vuu-16 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: TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRMJ

B: TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRMJ

hetero molecules

59.7 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)	42.440, 72.850, 55.540
Angle α, β, γ (deg.)	90.00, 107.75, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRMJ / TRNA (CYTIDINE(32)/URIDINE(32)-2'-O)-METHYLTRANSFERASE / TRNA CM32/UM32 METHYLTRANSFERASE / TRMJ Mass: 29420.516 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: P0AE01, tRNA (cytidine32/uridine32-2'-O)-methyltransferase
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.05 Å³/Da / Density % sol: 40.16 % / Description: NONE
Crystal grow	pH: 4.6 / Details: 0.02M NA/KPO4, 0.1M MES PH6.5, 20% PEG3350, pH 4.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 1.9→20 Å / Num. obs: 24619 / % possible obs: 99.9 % / Observed criterion σ(I): 3.4 / Redundancy: 4.2 % / R_merge(I) obs: 0.05 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 3.4 / % possible all: 91.9

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CND

4cnd

Resolution: 1.9→19.58 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22753	1242	5.1 %	RANDOM
R_work	0.18	-	-	-
obs	0.18236	23340	96.45 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 39.423 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.17 Å²	-0 Å²	-0.63 Å²
2-	-	-0.2 Å²	0 Å²
3-	-	-	1.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2481	0	59	43	2583

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	2600
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	2544
X-RAY DIFFRACTION	r_angle_refined_deg	1.495	1.986	3546
X-RAY DIFFRACTION	r_angle_other_deg	3.574	3	5828
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.329	5	332
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.337	24.375	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.501	15	414
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.92	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	431
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	2907
X-RAY DIFFRACTION	r_gen_planes_other	0.015	0.02	545
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.769	1.78	1343
X-RAY DIFFRACTION	r_mcbond_other	1.739	1.778	1342
X-RAY DIFFRACTION	r_mcangle_it	2.4	2.646	1670
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.512	2.127	1257
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.289	85	-
R_work	0.243	1575	-
obs	-	-	87.78 %

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	5.748	-2.622	1.9302	16.2681	6.7685	4.7828	0.3412	-0.3221	-0.7392	2.1812	0.0917	-0.4836	1.1335	-0.0409	-0.4329	0.7187	0.0225	-0.2123	0.1244	0.1919	0.4016	4.84	9.017	42.548
2	3.2922	0.5204	0.1351	5.8841	2.9276	3.2175	0.0162	-0.0938	0.0265	0.0911	-0.1675	0.5381	-0.019	-0.3846	0.1514	0.2447	-0.0065	0.0496	0.2003	0.0392	0.1277	-9.632	21.889	36.777
3	1.8547	-1.0803	-0.9138	4.9661	2.2306	2.5777	-0.0844	-0.0026	-0.1468	0.4889	0.0071	0.3914	0.272	-0.1421	0.0773	0.2631	-0.001	0.0662	0.1477	0.0618	0.0655	-6.617	16.995	38.763
4	14.5415	-11.6373	-6.5079	16.5584	9.3717	11.1269	0.1161	0.1941	-0.5693	0.1189	-0.072	1.6829	0.0557	-0.8046	-0.0442	0.1723	-0.0611	0.0231	0.1324	0.1428	0.4041	-17.236	14.587	34.84
5	2.9971	-4.1838	-3.8418	22.0381	9.9392	12.5452	-0.0838	0.0616	-0.1667	0.6499	-0.0592	0.6868	0.3269	-0.034	0.1431	0.2616	-0.0471	0.0922	0.1526	0.0978	0.1689	-10.029	11.629	41.273
6	6.6425	0.7444	-0.4981	2.8283	0.758	0.9145	-0.066	-0.4374	-0.0092	1.0073	0.1083	-0.0522	0.0905	-0.0492	-0.0423	0.463	0.0747	-0.0061	0.1714	0.032	0.036	-1.993	25.836	47.103
7	2.0877	1.7853	3.2628	8.9311	2.2656	5.1965	-0.2044	0.0057	0.002	-0.6284	0.271	-0.7406	-0.3506	-0.1201	-0.0665	0.1854	0.0447	0.1422	0.3018	0.1827	0.3658	7.595	36.47	34.899
8	2.9991	-0.6629	0.1775	3.6713	1.0964	1.387	0.0126	-0.1867	-0.0296	0.3953	0.2158	-0.3725	0.3335	0.2145	-0.2283	0.261	0.0364	-0.0432	0.177	0.0012	0.089	6.009	21.768	39.439
9	3.1141	-1.7035	-0.4886	4.2731	0.9824	1.549	-0.0509	-0.0305	0.072	0.1156	0.0965	0.0486	0.0013	-0.0878	-0.0457	0.2348	-0.0251	-0.0002	0.1949	0.0094	0.169	0.825	32.859	38.325
10	18.8328	-0.8278	-1.4467	12.3382	2.0364	1.7571	0.035	0.2142	0.8072	0.0055	0.1096	0.5702	-0.5048	-0.2809	-0.1447	0.2991	0.0283	-0.0018	0.135	0.0769	0.202	-0.316	32.067	19.911
11	6.4622	-1.8126	0.307	4.3622	0.7125	2.7365	0.0076	-0.0675	-0.1603	0.2571	0.1368	-0.2647	0.3123	0.1289	-0.1444	0.2549	0.0052	-0.0177	0.1766	0.0052	0.1141	4.737	16.035	31.593
12	5.9098	-4.1505	0.2164	26.3565	5.533	8.1107	-0.1158	0.567	0.4947	-1.5462	0.3705	-0.7269	-0.8544	0.6207	-0.2546	0.2255	-0.0809	0.0505	0.1994	0.1095	0.1555	7.262	29.859	10.762
13	5.9451	3.2009	-0.2101	6.9	-0.5665	2.6724	0.0115	0.0587	0.1179	-0.1947	-0.1506	0.1764	-0.0964	0.0361	0.139	0.2321	0.0186	0.0071	0.2336	0.038	0.1115	-3.766	14.985	10.481
14	6.3649	3.413	-0.5725	6.1446	0.4313	0.9056	0.0665	0.1161	0.2751	0.0689	-0.0776	0.2411	-0.1499	-0.0749	0.0112	0.2012	0.0137	0.0107	0.2013	0.0507	0.1106	-5.18	22.437	16.816
15	2.3629	0.8616	-0.1486	4.7815	0.0929	2.4959	-0.0416	0.1166	0.3496	-0.0723	-0.0427	0.6049	-0.1287	-0.3603	0.0844	0.1886	0.0249	-0.0327	0.2197	0.0373	0.1536	-11.992	16.458	9.362
16	2.4004	0.3838	0.2991	3.0161	0.4063	1.8076	-0.0599	0.1954	0.103	-0.2462	-0.062	0.2743	-0.1947	0.0857	0.1218	0.1813	0.0135	0.0139	0.2086	0.0519	0.0538	-4.082	16.688	7.975
17	0.282	1.3488	1.5077	11.1489	13.1679	15.7163	-0.3715	-0.105	-0.1456	0.0589	0.9267	-0.3556	0.3493	1.3494	-0.5552	1.2137	0.7279	0.3397	0.6234	0.0315	0.6169	4.413	-1.269	21.551
18	2.8919	-3.6317	-3.3202	15.225	7.0537	9.4293	0.0031	-0.0281	-0.4673	0.5854	-0.075	0.1773	0.615	-0.2599	0.0719	0.1607	0.0281	-0.0121	0.1954	0.034	0.1667	9.654	3.206	16.604
19	2.6807	0.5653	1.0545	3.0484	0.7646	1.8757	0.0193	0.312	0.1935	-0.1723	0.0304	-0.3557	-0.0781	0.4366	-0.0497	0.2015	0.0069	0.0464	0.2755	0.0522	0.1432	7.198	14.64	12.413
20	4.7035	0.2728	0.2462	2.859	-0.0347	2.0633	-0.0962	0.2909	-0.2341	-0.2049	0.0098	0.142	0.2644	0.0038	0.0863	0.2276	0.0432	0.0408	0.2131	0.0133	0.1184	1.223	2.922	12.233
21	11.2433	2.377	0.1788	9.2184	-4.5116	11.9921	0.0806	-0.464	-0.4691	0.6471	0.1034	0.4227	0.3243	-0.2045	-0.184	0.2828	0.0264	0.0074	0.1124	0.0347	0.1218	0.363	5.374	31.096
22	4.1754	0.4815	-0.2054	3.1409	-0.012	3.0028	-0.0544	0.1628	0.2252	0.0538	0.0296	-0.2555	-0.1685	0.1812	0.0248	0.2023	-0.0049	-0.0027	0.1979	0.0353	0.121	4.462	19.373	21.034

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-5 - 5
2	X-RAY DIFFRACTION	2	A	6 - 22
3	X-RAY DIFFRACTION	3	A	23 - 40
4	X-RAY DIFFRACTION	4	A	41 - 51
5	X-RAY DIFFRACTION	5	A	52 - 61
6	X-RAY DIFFRACTION	6	A	62 - 79
7	X-RAY DIFFRACTION	7	A	80 - 92
8	X-RAY DIFFRACTION	8	A	93 - 116
9	X-RAY DIFFRACTION	9	A	117 - 135
10	X-RAY DIFFRACTION	10	A	136 - 142
11	X-RAY DIFFRACTION	11	A	143 - 164
12	X-RAY DIFFRACTION	12	B	-5 - 2
13	X-RAY DIFFRACTION	13	B	3 - 14
14	X-RAY DIFFRACTION	14	B	15 - 31
15	X-RAY DIFFRACTION	15	B	32 - 46
16	X-RAY DIFFRACTION	16	B	47 - 80
17	X-RAY DIFFRACTION	17	B	81
18	X-RAY DIFFRACTION	18	B	87 - 93
19	X-RAY DIFFRACTION	19	B	94 - 116
20	X-RAY DIFFRACTION	20	B	117 - 133
21	X-RAY DIFFRACTION	21	B	134 - 140
22	X-RAY DIFFRACTION	22	B	141 - 164

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