PDB-5bxy: Crystal structure of RNA methyltransferase from Salinibacter rube...

ID or keywords:

Entry

Database: PDB / ID: 5bxy

Title

Crystal structure of RNA methyltransferase from Salinibacter ruber in complex with S-Adenosyl-L-homocysteine

Components

RNA methyltransferase

Keywords

TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

protein-lysine N-methyltransferase activity
Similarity search - Function

Biological species

Salinibacter ruber (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Handing, K.B. / LaRowe, C. / Shabalin, I.G. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal structure of RNA methylase family protein from Salinibacterruber in complex with S-Adenosyl-L-homocysteine.
Authors: Handing, K.B. / LaRowe, C. / Shabalin, I.G. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Almo, S.C. / Minor, W.

History

Deposition	Jun 9, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5bxy.cif.gz	139.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5bxy_validation.pdf.gz	692.4 KB	Display	wwPDB validaton report
Full document	5bxy_full_validation.pdf.gz	692.4 KB	Display
Data in XML	5bxy_validation.xml.gz	16.6 KB	Display
Data in CIF	5bxy_validation.cif.gz	25 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bx/5bxy ftp://data.pdbj.org/pub/pdb/validation_reports/bx/5bxy	HTTPS FTP

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Related structure data

Similar structure data	4qnq-3 5s3e-1 4qnq-9 5s1m-1 5dpw-5 2j16-2 5e0h-2 5hgt-d 7bf5-2 5s3s-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
Other databases	TargetTrack: NYSGRC-030807

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA methyltransferase

B: RNA methyltransferase

hetero molecules

36.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA methyltransferase

hetero molecules

defined by author&software
18.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: RNA methyltransferase

hetero molecules

defined by author&software
18.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.574, 86.040, 85.057
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	5 - 154
2	0	1	0	B	5 - 154

#1: Protein	RNA methyltransferase Mass: 17703.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salinibacter ruber (bacteria) / Strain: DSM 13855 / M31 / Gene: SRU_1020 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL References: UniProt: Q2S3S9, Transferases; Transferring one-carbon groups; Methyltransferases
#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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.27 Å³/Da / Density % sol: 45.81 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 #23 (0.1M Tris, 20%w/v PEG 8K, 0.2M ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 #23 (0.1M Tris, 20%w/v PEG 8K, 0.2M Magnesium Chloride, 6-Hydrate pH=8.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

Crystal

Density Matthews: 2.27 Å³/Da / Density % sol: 45.81 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 #23 (0.1M Tris, 20%w/v PEG 8K, 0.2M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2015
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. obs: 31176 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / R_merge(I) obs: 0.099 / R_sym value: 0.099 / Net I/av σ(I): 17.8 / Net I/σ(I): 17.8
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-2000		data scaling
SCALEPACK		data scaling
HKL-3000		data reduction
MLPHARE		phasing
HKL-3000		phasing
DM		phasing
SHELX		phasing
PDB_EXTRACT	3.15	data extraction
REFMAC	5.8.0107	refinement
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.75→50 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.134 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1882	1508	4.8 %	RANDOM
R_work	0.1484	-	-	-
obs	0.1503	29629	94.61 %	-

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 max: 155.17 Å² / B_iso mean: 20.852 Å² / B_iso min: 5.61 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0 Å²	0 Å²	0 Å²
2-	-	0.13 Å²	-0 Å²
3-	-	-	-0.13 Å²

Refinement step

Cycle: final / Resolution: 1.75→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2348	0	56	341	2745
B_iso mean	-	-	14.19	31.8	-
Num. residues	-	-	-	-	308

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	2473
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	2345
X-RAY DIFFRACTION	r_angle_refined_deg	1.598	2.015	3388
X-RAY DIFFRACTION	r_angle_other_deg	1.206	3	5392
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.292	5	311
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.87	23.365	104
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.765	15	369
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.814	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	398
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2759
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	508
X-RAY DIFFRACTION	r_mcbond_it	4.007	0.528	1242
X-RAY DIFFRACTION	r_mcbond_other	3.98	0.526	1241
X-RAY DIFFRACTION	r_mcangle_it	4.481	0.762	1547

Refine LS restraints NCS

Ens-ID: 1 / Number: 17258 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.752→1.798 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.274	120	-
R_work	0.211	2159	-
all	-	2279	-
obs	-	-	95.4 %

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	2.346	0.5431	-0.5367	2.6438	1.6356	1.9432	0.0087	0.0699	-0.0524	-0.0937	0.033	-0.0687	-0.1005	0.0812	-0.0417	0.099	-0.0092	0.0046	0.0948	0.0027	0.0611	12.269	21.019	52.429
2	5.2513	-1.4837	-5.4024	9.4197	9.2508	15.4523	-0.1863	0.213	-0.0676	0.3616	-0.2766	0.7075	0.2413	-0.7636	0.4629	0.0764	-0.0015	0.0007	0.1578	-0.0342	0.1317	-2.183	17.673	58.088
3	1.6515	-0.6954	-0.4635	1.8522	0.1798	2.8539	-0.071	0.0126	-0.0386	0.0704	0.0025	0.0942	-0.0643	-0.1697	0.0686	0.0811	0.0079	-0.001	0.0695	-0.0221	0.0449	7.391	22.754	62.447
4	8.4432	-3.2566	-0.4975	6.0175	0.13	2.1423	0.2254	0.2496	0.382	-0.1585	-0.1008	-0.386	-0.3377	0.2371	-0.1246	0.1305	-0.0215	-0.0036	0.0821	-0.0217	0.0557	17.809	29.952	63.984
5	1.5627	-0.4756	-0.4883	1.4576	0.5724	0.938	-0.0684	-0.1744	-0.0204	0.1963	0.041	-0.0237	0.0562	0.0232	0.0274	0.1081	0.0075	-0.0034	0.0812	-0.0103	0.0066	11.318	19.332	68.213
6	1.4149	0.8507	-1.7362	3.109	-1.2253	2.4913	-0.0807	-0.1529	-0.1681	0.0674	0.0255	-0.1343	0.2658	0.2449	0.0552	0.1621	0.0262	-0.0253	0.1055	-0.007	0.123	16.88	7.912	59.786
7	2.063	-0.0763	0.4419	1.7032	0.6431	1.9805	-0.0368	0.0522	-0.1007	0.0378	-0.0033	0.1553	0.2753	0.0086	0.0402	0.1192	-0.0275	0.0285	0.0558	-0.0085	0.0746	7.269	7.117	56.054
8	16.9318	-1.9346	-11.0356	19.9948	-15.9099	22.1055	0.1029	0.5982	-1.4295	1.1691	-0.7696	0.4331	-1.0696	0.2175	0.6667	0.6184	0.0923	-0.1166	0.166	-0.0135	0.5829	7.553	-5.405	63.711
9	5.1407	-0.8105	4.8958	5.151	-2.8548	13.6235	0.009	-0.0783	-0.384	-0.0458	0.0823	0.232	0.3201	-0.206	-0.0914	0.0846	0.0063	0.0348	0.0693	0.0234	0.0861	27.548	-10.442	48.408
10	1.9865	-0.5925	-0.0923	1.6624	-0.3938	1.6649	-0.0192	0.0349	-0.2075	-0.0807	0.0031	0.0657	0.0882	-0.1071	0.0161	0.0673	0.0052	0.0057	0.0575	-0.011	0.0324	32.628	-7.222	39.884
11	2.2264	2.1065	2.4218	4.8708	2.6058	5.6853	0.1547	0.0205	-0.2085	0.0592	-0.1082	-0.0804	0.3661	-0.1124	-0.0464	0.0721	0.0264	0.0118	0.0952	-0.0192	0.1005	37.172	-9.335	40.669
12	1.0876	0.278	0.6789	6.6295	2.4283	2.7914	0.0693	0.027	-0.1526	0.1653	0.0135	-0.4498	0.2666	0.2417	-0.0828	0.0485	0.0297	0.0252	0.0965	-0.002	0.1164	43.779	-9.281	41.866
13	24.3639	11.8867	16.7874	8.5229	7.3494	22.3931	-0.4721	0.8329	0.0955	-0.3227	0.3249	-0.2213	-0.3377	0.6209	0.1473	0.1024	-0.0196	0.0329	0.1433	0.0037	0.0949	39.841	4.59	35.701
14	1.305	-0.0374	0.0154	1.2324	0.0953	0.0293	-0.0415	-0.0893	0.0516	0.0679	0.0099	0.0527	-0.0241	0.0193	0.0316	0.0943	0.0009	-0.0036	0.1051	0.0095	0.0492	29.182	5.519	44.727
15	11.1054	-2.6118	5.0955	8.742	-3.1486	17.9	0.1494	-0.6008	-0.6551	0.0156	0.1872	0.6205	0.8734	-0.5299	-0.3366	0.0957	-0.013	0.0268	0.0957	0.0325	0.1288	19.887	-2.83	49.679
16	3.8353	1.2134	-1.5823	0.6773	-0.0245	3.6241	0.19	-0.2319	0.558	0.0216	0.0303	0.198	-0.6739	-0.0509	-0.2203	0.1815	0.0211	0.024	0.1228	-0.0264	0.1131	23.489	13.983	40.771

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 16
2	X-RAY DIFFRACTION	2	A	17 - 23
3	X-RAY DIFFRACTION	3	A	24 - 53
4	X-RAY DIFFRACTION	4	A	54 - 68
5	X-RAY DIFFRACTION	5	A	69 - 94
6	X-RAY DIFFRACTION	6	A	95 - 109
7	X-RAY DIFFRACTION	7	A	110 - 149
8	X-RAY DIFFRACTION	8	A	150 - 155
9	X-RAY DIFFRACTION	9	B	5 - 17
10	X-RAY DIFFRACTION	10	B	18 - 39
11	X-RAY DIFFRACTION	11	B	40 - 56
12	X-RAY DIFFRACTION	12	B	57 - 83
13	X-RAY DIFFRACTION	13	B	84 - 89
14	X-RAY DIFFRACTION	14	B	90 - 132
15	X-RAY DIFFRACTION	15	B	133 - 144
16	X-RAY DIFFRACTION	16	B	145 - 157

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