PDB-3g8q: A cytidine deaminase edits C-to-U in transfer RNAs in archaea

ID or keywords:

Entry

Database: PDB / ID: 3g8q

Title

A cytidine deaminase edits C-to-U in transfer RNAs in archaea

Components

Predicted RNA-binding protein, contains THUMP domain

Keywords

RNA BINDING PROTEIN / cytidine deaminase / THUMP / ferredoxin-like domain

Function / homology

Function and homology information

tRNA(cytosine8) deaminase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines / cytidine to uridine editing / tRNA modification / tRNA binding / protein homodimerization activity / zinc ion binding / identical protein binding
Similarity search - Function

Biological species

Methanopyrus kandleri (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2.4 Å

Authors

Xiong, Y. / Stanley, B.J.

Citation

Journal: Science / Year: 2009
Title: A cytidine deaminase edits C to U in transfer RNAs in Archaea
Authors: Randau, L. / Stanley, B.J. / Kohlway, A. / Mechta, S. / Xiong, Y. / Soll, D.

History

Deposition	Feb 12, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	3g8q.cif.gz	440.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3g8q.ent.gz	369.2 KB	Display	PDB format
PDBx/mmJSON format	3g8q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3g8q_validation.pdf.gz	463.2 KB	Display	wwPDB validaton report
Full document	3g8q_full_validation.pdf.gz	516.2 KB	Display
Data in XML	3g8q_validation.xml.gz	47.5 KB	Display
Data in CIF	3g8q_validation.cif.gz	65.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g8/3g8q ftp://data.pdbj.org/pub/pdb/validation_reports/g8/3g8q	HTTPS FTP

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Related structure data

Similar structure data	6kos-d 2i30-d 5id7-2 4wqo-d 4ct6-d 4cru-d 2bxq-d 4fme-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) 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: Predicted RNA-binding protein, contains THUMP domain

B: Predicted RNA-binding protein, contains THUMP domain

C: Predicted RNA-binding protein, contains THUMP domain

D: Predicted RNA-binding protein, contains THUMP domain

hetero molecules

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

1

A: Predicted RNA-binding protein, contains THUMP domain

D: Predicted RNA-binding protein, contains THUMP domain

hetero molecules

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

2

B: Predicted RNA-binding protein, contains THUMP domain

C: Predicted RNA-binding protein, contains THUMP domain

hetero molecules

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

Unit cell

Length a, b, c (Å)	184.465, 77.060, 109.082
Angle α, β, γ (deg.)	90.00, 103.57, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Predicted RNA-binding protein, contains THUMP domain Mass: 30657.918 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: MK0935 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TWU6
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.07 Å³/Da / Density % sol: 59.97 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.1 M Na cacodylate, 32-40% PEG 400, 0.1 M Ca acetate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 55130

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Processing

Software

Name	Version	Classification
REFMAC	5.4.0077	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MIR / Resolution: 2.4→30 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.922 / SU B: 22.231 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26482	2938	5.1 %	RANDOM
R_work	0.2018	-	-	-
obs	0.20496	55116	99.42 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 60.679 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	-0.28 Å²
2-	-	0 Å²	0 Å²
3-	-	-	-0.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8587	0	11	189	8787

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	8719
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	8405
X-RAY DIFFRACTION	r_angle_refined_deg	1.217	1.993	11826
X-RAY DIFFRACTION	r_angle_other_deg	1.088	3	19344
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.57	5	1105
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.533	22.688	413
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.808	15	1479
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.987	15	113
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	1369
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	9804
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1813
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	1.789	4	5505
X-RAY DIFFRACTION	r_mcbond_other	0	4	2262
X-RAY DIFFRACTION	r_mcangle_it	2.91	6	8900
X-RAY DIFFRACTION	r_scbond_it	3.354	6	3214
X-RAY DIFFRACTION	r_scangle_it	5.382	9	2926
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	209	-
R_work	0.309	4029	-
obs	-	-	99.69 %

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	5.0289	-1.1349	-1.232	4.1183	0.3107	4.8724	0.2715	0.3625	0.301	-0.0316	-0.0024	0.4051	-0.88	-0.831	-0.2691	0.2694	0.1948	0.0011	0.2019	0.0913	0.175	-23.9647	31.7201	37.3047
2	1.908	-0.6011	-1.6708	4.0813	0.7919	1.5165	0.2659	0.3835	0.2437	0.1183	0.0033	0.3301	-0.2575	-0.3179	-0.2692	0.2378	0.0641	0.0288	0.1637	0.0451	0.2866	-16.3548	22.6155	36.4167
3	0.5605	0.7984	-0.6139	3.0532	-0.4968	3.2121	0.0024	0.1545	-0.0003	-0.2052	0.1188	0.3561	-0.2767	-0.3066	-0.1212	0.1007	0.0235	-0.0985	0.1522	-0.009	0.1884	-16.5934	1.6526	33.2107
4	1.4814	0.6635	-0.4471	5.8321	1.4727	7.0869	0.0128	0.1583	-0.2078	-0.2022	0.0163	-0.1624	0.4369	0.0685	-0.0291	0.0692	0.0078	-0.0513	0.0394	-0.0146	0.1305	-11.7337	-16.1989	38.4671
5	3.2585	-0.4935	-4.5538	4.7876	0.4561	6.486	-0.1184	-0.0151	-0.4318	0.2088	-0.2891	-0.282	0.2687	0.1574	0.4075	0.1339	0.1236	-0.2175	0.4616	-0.0936	0.5281	39.7974	20.9786	12.1406
6	3.2725	-0.8133	-2.0774	4.2341	2.0756	2.9392	0.3556	0.3151	0.0284	-0.0778	-0.1434	-0.3057	-0.2427	0.1288	-0.2121	0.0711	0.1038	-0.0282	0.3787	-0.0083	0.2642	39.2546	32.7621	7.438
7	3.8297	0.9012	0.0102	5.4831	-2.0587	6.1136	0.2072	0.1611	0.2291	0.3218	-0.3948	-0.7861	-0.7787	0.8957	0.1877	0.1577	-0.169	-0.1389	0.5359	0.1165	0.5261	34.4389	54.0908	10.2884
8	2.4063	-1.8018	1.0308	4.046	-0.125	4.9876	-0.2189	-0.1803	0.9898	1.0489	0.0009	-0.5714	-2.111	0.6044	0.218	1.5071	-0.5049	-0.0261	0.3696	0.0259	0.6553	38.3153	72.6768	18.3416
9	8.1866	-5.8785	3.5245	7.4547	-7.3377	9.4306	0.4143	-0.1178	0.3825	0.761	-0.0654	-0.107	-1.4736	0.4856	-0.3489	0.4721	-0.1506	-0.0215	0.1756	-0.0413	0.2746	38.3964	67.3363	17.872
10	4.9245	-0.0597	-0.9732	3.412	-1.0371	3.4336	0.2846	-0.21	-0.0273	0.4922	-0.3133	-0.1064	0.0125	0.3052	0.0288	0.1229	-0.0313	-0.0696	0.1827	0.0162	0.173	25.6414	32.6352	28.8329
11	3.7733	0.0495	-2.5084	1.8102	-0.2841	6.7181	-0.309	-0.0605	0.0569	0.3936	0.1098	0.1278	-0.1561	0.43	0.1993	0.1746	0.0351	-0.105	0.2509	-0.011	0.3235	11.924	50.4807	16.9324
12	7.4945	1.3984	2.4236	1.2354	-0.0244	8.1538	-0.2711	-0.9811	0.334	0.0551	0.0054	0.0746	-0.3368	-1.348	0.2656	0.0608	0.1597	-0.0758	0.5556	-0.0844	0.4199	-5.1519	51.0422	14.9753
13	5.5882	-0.9444	1.2623	1.714	-1.4464	6.2806	-0.3024	-0.4961	0.1144	-0.2397	0.1274	0.2989	-0.4184	-1.1713	0.175	0.3013	0.0934	-0.1333	0.5348	-0.0696	0.4826	-9.8181	51.2165	4.6562
14	3.003	-4.2672	-0.1407	12.402	-2.7014	3.2147	-0.0694	-0.0771	0.0724	0.0697	0.065	0.0806	-0.2544	-0.1888	0.0044	0.0562	0.0152	-0.0528	0.1399	-0.0043	0.1111	-2.4168	48.2249	11.6196
15	4.8351	-2.4685	-2.9931	5.4239	3.5628	3.2563	0.3466	0.363	0.4381	-0.3344	0.029	0.0116	-0.709	0.0027	-0.3755	0.556	-0.0881	0.1489	0.161	0.0318	0.2637	0.6755	30.448	30.7214
16	1.4959	0.4782	-1.3933	1.9135	0.6686	4.1974	0.2762	-0.0936	0.0053	0.0223	-0.1412	-0.1937	-0.3266	0.2498	-0.135	0.2114	-0.0635	-0.0123	0.0789	0.0009	0.1149	3.037	24.1061	39.9696
17	2.5451	0.1084	-0.2673	0.5524	-0.0739	2.9418	0.0796	-0.0283	-0.0462	-0.1326	0.0477	-0.1208	0.233	0.1578	-0.1273	0.2161	-0.0124	-0.041	0.098	-0.0143	0.0544	7.1011	8.5659	16.0618
18	2.8744	-0.4347	0.6472	1.8803	1.5311	4.5841	0.207	0.1238	-0.0768	-0.142	-0.0078	-0.131	0.4196	0.2453	-0.1993	0.1866	0.0585	-0.0446	0.1586	0.0026	0.0337	10.8485	8.844	-1.2396

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 75
2	X-RAY DIFFRACTION	2	A	76 - 115
3	X-RAY DIFFRACTION	3	A	116 - 204
4	X-RAY DIFFRACTION	4	A	205 - 278
5	X-RAY DIFFRACTION	5	B	1 - 33
6	X-RAY DIFFRACTION	6	B	34 - 115
7	X-RAY DIFFRACTION	7	B	116 - 183
8	X-RAY DIFFRACTION	8	B	184 - 260
9	X-RAY DIFFRACTION	9	B	261 - 277
10	X-RAY DIFFRACTION	10	C	1 - 109
11	X-RAY DIFFRACTION	11	C	110 - 183
12	X-RAY DIFFRACTION	12	C	184 - 216
13	X-RAY DIFFRACTION	13	C	217 - 263
14	X-RAY DIFFRACTION	14	C	264 - 277
15	X-RAY DIFFRACTION	15	D	1 - 23
16	X-RAY DIFFRACTION	16	D	24 - 115
17	X-RAY DIFFRACTION	17	D	116 - 212
18	X-RAY DIFFRACTION	18	D	213 - 277

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