PDB-3tqs: Structure of the dimethyladenosine transferase (ksgA) from Coxiel...

ID or keywords:

Entry

Database: PDB / ID: 3tqs

Title

Structure of the dimethyladenosine transferase (ksgA) from Coxiella burnetii

Components

Ribosomal RNA small subunit methyltransferase A

Keywords

TRANSFERASE / Protein synthesis

Function / homology

Function and homology information

16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / RNA binding / cytosol
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.98 Å

Authors

Rudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Oct 21, 2015	Group: Database references
Revision 1.3	Feb 10, 2016	Group: Database references
Revision 1.4	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tqs.cif.gz	411.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3tqs.ent.gz	335.3 KB	Display	PDB format
PDBx/mmJSON format	3tqs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tqs_validation.pdf.gz	430.9 KB	Display	wwPDB validaton report
Full document	3tqs_full_validation.pdf.gz	439.1 KB	Display
Data in XML	3tqs_validation.xml.gz	50.6 KB	Display
Data in CIF	3tqs_validation.cif.gz	72.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqs ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqs	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	2q7t-1 6xwh-d 4e8b-d 4n13-d 2q7u-1 5gg7-2 3gt0-d 2wcw-1 4ypn-d 3omg-2 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribosomal RNA small subunit methyltransferase A

B: Ribosomal RNA small subunit methyltransferase A

C: Ribosomal RNA small subunit methyltransferase A

D: Ribosomal RNA small subunit methyltransferase A

119 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribosomal RNA small subunit methyltransferase A

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

2

B: Ribosomal RNA small subunit methyltransferase A

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

3

C: Ribosomal RNA small subunit methyltransferase A

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

4

D: Ribosomal RNA small subunit methyltransferase A

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

Unit cell

Length a, b, c (Å)	38.007, 57.895, 112.938
Angle α, β, γ (deg.)	90.000, 90.010, 104.340
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ribosomal RNA small subunit methyltransferase A / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine ...16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase Mass: 29663.455 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: rsmA, ksgA, CBU_1982 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q83AC2, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1104 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.38 %
Crystal grow	Temperature: 293 K / Method: sitting drop / pH: 7.5 Details: 200 mM NaCl, 20% PEG 3350, pH 7.5, sitting drop, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X4C / Wavelength: 0.979 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 11, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.98→50 Å / Num. all: 64960 / Num. obs: 60608 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / R_merge(I) obs: 0.03 / Χ²: 0.99 / Net I/σ(I): 12.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.98-2.01	1.9	0.066	2189	0.963	1	67.5
2.01-2.05	1.9	0.063	2769	0.889	1	86.1
2.05-2.09	2	0.059	3023	0.979	1	92.4
2.09-2.13	2	0.052	3039	0.971	1	93.1
2.13-2.18	2	0.048	2979	0.901	1	93.4
2.18-2.23	2	0.047	3108	0.914	1	93.6
2.23-2.29	2	0.046	2967	0.983	1	93.4
2.29-2.35	2	0.041	3075	0.922	1	94
2.35-2.42	2	0.039	3079	0.871	1	94.4
2.42-2.49	2	0.039	3062	0.974	1	94.9
2.49-2.58	2	0.038	3090	0.942	1	95
2.58-2.69	2	0.032	3119	0.98	1	95.4
2.69-2.81	2	0.034	3083	1.054	1	95.7
2.81-2.96	2	0.031	3158	0.952	1	96
2.96-3.14	2	0.03	3107	0.955	1	96
3.14-3.39	2	0.025	3165	0.995	1	97
3.39-3.73	2	0.023	3130	1.07	1	96.8
3.73-4.26	2	0.021	3203	1.131	1	97.3
4.26-5.37	2	0.021	3179	1.072	1	98.2
5.37-50	2	0.023	3084	1.246	1	95.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.98→17.75 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5533 / SU ML: 0.2 / σ(F): 1.97 / Phase error: 44.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2458	3048	5.05 %
R_work	0.1835	-	-
obs	0.1866	60349	92.89 %
all	-	63397	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.176 Å² / k_sol: 0.393 e/Å³

Displacement parameters

B_iso max: 64.98 Å² / B_iso mean: 14.8759 Å² / B_iso min: 2.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.4574 Å²	-0.842 Å²	-0.5942 Å²
2-	-	-1.684 Å²	-0.2148 Å²
3-	-	-	3.1414 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→17.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7996	0	0	1104	9100

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8184
X-RAY DIFFRACTION	f_angle_d	1	11124
X-RAY DIFFRACTION	f_chiral_restr	0.07	1276
X-RAY DIFFRACTION	f_plane_restr	0.004	1436
X-RAY DIFFRACTION	f_dihedral_angle_d	14.212	3060

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.98-2.0494	0.2787	272	0.1789	4595	4867	76
2.0494-2.1314	0.2452	297	0.1737	5775	6072	93
2.1314-2.2282	0.2393	299	0.1841	5763	6062	93
2.2282-2.3454	0.2525	292	0.1775	5784	6076	94
2.3454-2.492	0.2443	324	0.1746	5796	6120	95
2.492-2.6838	0.2666	317	0.1822	5863	6180	95
2.6838-2.9528	0.2643	293	0.1892	5944	6237	96
2.9528-3.3775	0.2569	325	0.1937	5926	6251	96
3.3775-4.2456	0.2309	336	0.1832	5968	6304	97
4.2456-17.75	0.2175	293	0.1859	5887	6180	95

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	0.0112	-0.0107	0.0069	0.0089	-0.0068	0.0036	0.0056	0.0299	0.0152	0.0001	-0.0017	-0.0067	-0.0099	-0.0313	0.0156	-0.0717	0.0313	-0.0164	0.102	0.0072	0.0218	-21.0621	54.1862	21.0029
2	0.0045	0.0016	0.0002	0.0071	0.0023	0.0021	0.03	-0.0208	-0.0135	0.026	-0.0261	-0.008	-0.0022	-0.0061	0.0074	-0.0123	-0.0375	0.013	0.0587	0.0056	0.0752	-18.6744	56.5172	35.0531
3	0.0197	0.0144	0.0018	0.0334	0.0026	-0	0.028	0.0123	0.0497	0.0134	-0.0058	-0.0182	-0.0022	0.0024	0.0075	0.0422	0.0179	-0.0216	-0.0273	0.0316	0.0681	-12.0635	43.7183	26.2468
4	0.0169	-0.0137	0.0045	0.025	-0.022	0.0181	-0.0181	-0.0162	-0.0009	0.0064	0.0047	-0.0175	0.0159	0.0193	-0.0141	0.008	0.0541	-0.0294	-0.0522	0.0434	0.064	-7.3122	40.2989	18.9512
5	0.0167	0.0177	-0.0028	0.0274	-0.0009	0.002	-0.0299	-0.0265	0.0022	0.0432	0.004	-0.0576	-0.0275	-0.0102	-0.008	-0.0128	0.091	-0.058	0.012	0.0775	0.0399	3.7252	23.503	27.4402
6	0.0243	0.0095	0.0023	0	0.0006	0.0019	0.0354	-0.0332	0.0066	0.018	-0.0067	-0.0015	0.0149	0.0153	0.0636	-0.1422	-0.0751	-0.0219	0.0901	0.0493	-0.0265	12.6724	53.6966	55.0385
7	0.0207	-0.0035	-0.0092	0.0126	0.0058	0.0053	0.0157	0.0305	-0.0641	0.0284	-0.0377	0.0097	-0.0032	-0.0161	-0.0224	0.0487	-0.1142	-0.0797	0.0811	-0.0205	0.0291	6.5604	65.9677	56.5838
8	0.0045	0.0055	0.0001	0.0069	0.0001	0	0.0159	0.0017	0.0123	-0.0008	0.0035	0.009	-0.008	-0.0042	0.005	0.0429	-0.036	-0.0027	0.0662	0.0261	0.0154	-6.2249	72.1538	44.2135
9	0.0395	-0.0003	-0.013	0.0167	0.0024	0.0023	-0.025	0.0163	-0.02	0.0053	0.0311	0.0328	0.0236	-0.048	0.0033	0.0428	-0.0536	0.0682	0.0434	0.0322	0.0541	1.5264	68.6822	47.7794
10	0.0153	-0.0054	0.0043	0.0246	0.0087	0.0041	0.0046	-0.0403	-0.0027	0.0074	0.0088	0.0637	-0.0033	-0.001	0.0042	-0.0908	0.0073	-0.0092	0.0578	-0.0018	0.0251	-10.8616	86.2967	55.6758
11	0.001	-0.0021	0.0006	0.0046	-0.0017	0.0012	0.0117	0.0013	0.008	-0.0229	0.0026	-0.0167	-0.0229	0.003	-0.0001	0.0876	-0.0417	-0.009	-0.0206	-0.0003	0.0435	-21.0685	54.181	77.4705
12	0.0158	0.01	-0.0083	0.0143	0.0006	0.0081	0.0083	-0.0141	-0.0081	0.01	-0.0168	0.0106	-0.0152	-0.0045	0.0031	0.0871	0.0283	-0.01	0.0523	-0.0274	0.0266	-18.2773	57.1258	91.3263
13	0.085	-0.0066	-0.013	0.0232	-0.0024	0.0205	-0.0157	0.0105	0.0346	-0.0023	-0.0277	0.013	0.0306	-0.0386	-0.0211	0.038	-0.02	0.0141	0.1014	-0.0294	0.0174	-9.945	42.0107	81.3169
14	0.035	0.0105	0.0029	0.0163	0.0034	0.0021	-0.0153	0.0404	-0.0139	0.0264	0.0259	-0.0067	0.0044	0.0775	-0.0003	0.0676	-0.0242	0.0039	0.1086	-0.0078	0.004	-9.3939	41.6496	75.751
15	0.0078	0.0068	-0.0014	0.0524	-0.0218	0.029	-0.0068	-0.0292	0.007	0.0376	-0.01	-0.0858	-0.003	0.0393	0.0007	0.0717	-0.0473	0.008	0.007	-0.0167	0.0767	3.7173	23.4871	83.9181
16	0.0221	-0.0079	0.008	0.0097	0.0032	0.0079	-0.0079	0.0336	-0.0577	-0.012	-0.0198	0.0403	0.0126	-0.001	-0.0005	0.145	0.0272	0.0236	0.022	-0.0469	0.1082	12.5555	54.7437	-5.0569
17	0.0004	-0.0001	-0.005	0.0008	0.0032	0.0859	0.0004	-0.0218	0.0439	0.0099	-0.0123	0.0106	0.0623	0.028	-0.0072	0.0599	0.0606	0.0036	-0.0015	-0.0111	0.0862	13.62	56.7881	5.2767
18	0	-0.0033	-0.0008	0.0257	0.0135	0.0048	0.0104	0.0398	-0.0551	-0.0048	-0.0236	0.0395	-0.0054	-0.0267	0.0326	0.0525	0.1146	0.0671	0.0292	0.0021	0.0483	2.2094	66.2436	-2.5283
19	0.0119	-0.0036	0.0044	0.0277	0.0167	0.0115	-0.0022	-0.0026	0.0069	0.0146	0.0114	-0.0024	-0.0464	-0.0149	0.0041	0.06	0.0391	-0.0242	0.0256	-0.055	0.0652	0.1601	69.5087	-9.2814
20	0.0079	0.0024	0.0051	0.0225	0.0047	0.0037	-0.0272	-0.0044	-0.0011	0.0246	-0.0157	0.0547	0.0271	-0.0143	0.0003	0.1623	-0.0164	0.0227	0.0078	-0.0558	0.1052	-10.8761	86.3173	-0.7905

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 12:58)	A	12 - 58
2	X-RAY DIFFRACTION	2	(chain A and resid 59:96)	A	59 - 96
3	X-RAY DIFFRACTION	3	(chain A and resid 97:139)	A	97 - 139
4	X-RAY DIFFRACTION	4	(chain A and resid 140:197)	A	140 - 197
5	X-RAY DIFFRACTION	5	(chain A and resid 198:258)	A	198 - 258
6	X-RAY DIFFRACTION	6	(chain B and resid 12:90)	B	12 - 90
7	X-RAY DIFFRACTION	7	(chain B and resid 91:136)	B	91 - 136
8	X-RAY DIFFRACTION	8	(chain B and resid 137:149)	B	137 - 149
9	X-RAY DIFFRACTION	9	(chain B and resid 150:197)	B	150 - 197
10	X-RAY DIFFRACTION	10	(chain B and resid 198:258)	B	198 - 258
11	X-RAY DIFFRACTION	11	(chain C and resid 12:58)	C	12 - 58
12	X-RAY DIFFRACTION	12	(chain C and resid 59:94)	C	59 - 94
13	X-RAY DIFFRACTION	13	(chain C and resid 95:152)	C	95 - 152
14	X-RAY DIFFRACTION	14	(chain C and resid 153:197)	C	153 - 197
15	X-RAY DIFFRACTION	15	(chain C and resid 198:258)	C	198 - 258
16	X-RAY DIFFRACTION	16	(chain D and resid 12:66)	D	12 - 66
17	X-RAY DIFFRACTION	17	(chain D and resid 67:106)	D	67 - 106
18	X-RAY DIFFRACTION	18	(chain D and resid 107:139)	D	107 - 139
19	X-RAY DIFFRACTION	19	(chain D and resid 140:197)	D	140 - 197
20	X-RAY DIFFRACTION	20	(chain D and resid 198:258)	D	198 - 258

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