PDB-5irg: Reverse transcriptase domain of group II intron maturase from Ros...

ID or keywords:

Entry

Database: PDB / ID: 5irg

Title

Reverse transcriptase domain of group II intron maturase from Roseburia intestinalis in P212121 space group

Components

Retron-type reverse transcriptase

Keywords

RNA BINDING PROTEIN / Group II intron / maturase / reverse transcriptase

Function / homology

Function and homology information

RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / defense response to virus / RNA binding
Similarity search - Function

Biological species

Roseburia intestinalis XB6B4 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Zhao, C. / Pyle, A.M.

Funding support

United States, 1items

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution.
Authors: Zhao, C. / Pyle, A.M.

History

Deposition	Mar 13, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 25, 2016	Group: Database references
Revision 1.2	Jun 22, 2016	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Revision 1.6	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5irg.cif.gz	473.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5irg.ent.gz	395.9 KB	Display	PDB format
PDBx/mmJSON format	5irg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5irg_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	5irg_full_validation.pdf.gz	457.4 KB	Display
Data in XML	5irg_validation.xml.gz	42.5 KB	Display
Data in CIF	5irg_validation.cif.gz	58.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ir/5irg ftp://data.pdbj.org/pub/pdb/validation_reports/ir/5irg	HTTPS FTP

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Related structure data

Related structure data	5hhjSC 5hhkC 5hhlC 5irfC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hhk-d 5hhl-4 4bcq-1 5hhj-d 5irf-2 5hhl-1 5irf-1 6kui-d 4uub-d 4bck-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
Related items in Molecule of the Month	#65 - May 2005 Self-splicing RNA similarity (1) #227 - Nov 2018 Telomerase similarity (1)

Deposited unit

A: Retron-type reverse transcriptase

B: Retron-type reverse transcriptase

C: Retron-type reverse transcriptase

D: Retron-type reverse transcriptase

hetero molecules

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

1

A: Retron-type reverse transcriptase

D: Retron-type reverse transcriptase

hetero molecules

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

2

B: Retron-type reverse transcriptase

C: Retron-type reverse transcriptase

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.810, 145.350, 200.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Retron-type reverse transcriptase Mass: 35574.637 Da / Num. of mol.: 4 / Fragment: UNP residues 1-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseburia intestinalis XB6B4 (bacteria) Gene: RO1_37670 / Production host: Escherichia coli (E. coli) / References: UniProt: D4L313
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.23 Å³/Da / Density % sol: 44.8 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM MMT pH 8.0, 25% PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.3→49.135 Å / Num. obs: 57600 / % possible obs: 99.8 % / Redundancy: 7.1 % / Net I/σ(I): 16.9
Reflection shell	Highest resolution: 2.3 Å

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2254: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HHJ

5hhj

Resolution: 2.3→49.135 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 23.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2306	2841	4.98 %
R_work	0.1906	-	-
obs	0.1926	54596	99.88 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→49.135 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9190	0	4	304	9498

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9359
X-RAY DIFFRACTION	f_angle_d	0.43	12597
X-RAY DIFFRACTION	f_dihedral_angle_d	13.202	5779
X-RAY DIFFRACTION	f_chiral_restr	0.041	1384
X-RAY DIFFRACTION	f_plane_restr	0.003	1647

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.3262	0.3222	178	0.2886	3413	X-RAY DIFFRACTION	100
2.3262-2.3535	0.2821	188	0.2718	3417	X-RAY DIFFRACTION	100
2.3535-2.3822	0.3245	178	0.2707	3408	X-RAY DIFFRACTION	100
2.3822-2.4124	0.3263	168	0.2613	3350	X-RAY DIFFRACTION	100
2.4124-2.4441	0.3141	183	0.2632	3391	X-RAY DIFFRACTION	100
2.4441-2.4776	0.3085	182	0.2561	3347	X-RAY DIFFRACTION	100
2.4776-2.513	0.274	179	0.2454	3483	X-RAY DIFFRACTION	100
2.513-2.5505	0.3091	176	0.2453	3347	X-RAY DIFFRACTION	100
2.5505-2.5904	0.3033	179	0.2469	3390	X-RAY DIFFRACTION	100
2.5904-2.6328	0.2875	178	0.2348	3381	X-RAY DIFFRACTION	100
2.6328-2.6782	0.2903	181	0.2313	3458	X-RAY DIFFRACTION	100
2.6782-2.7269	0.2554	170	0.2232	3345	X-RAY DIFFRACTION	100
2.7269-2.7794	0.2379	185	0.2133	3358	X-RAY DIFFRACTION	100
2.7794-2.8361	0.2277	176	0.2049	3441	X-RAY DIFFRACTION	100
2.8361-2.8977	0.2618	174	0.2096	3350	X-RAY DIFFRACTION	100
2.8977-2.9651	0.2996	169	0.2234	3393	X-RAY DIFFRACTION	100
2.9651-3.0393	0.2937	178	0.2144	3439	X-RAY DIFFRACTION	100
3.0393-3.1215	0.2544	175	0.2033	3355	X-RAY DIFFRACTION	100
3.1215-3.2133	0.2189	180	0.1908	3402	X-RAY DIFFRACTION	100
3.2133-3.317	0.2795	178	0.1922	3407	X-RAY DIFFRACTION	100
3.317-3.4355	0.2049	181	0.186	3341	X-RAY DIFFRACTION	100
3.4355-3.573	0.2159	188	0.1824	3447	X-RAY DIFFRACTION	100
3.573-3.7356	0.2179	172	0.1689	3340	X-RAY DIFFRACTION	100
3.7356-3.9324	0.1757	178	0.1568	3424	X-RAY DIFFRACTION	100
3.9324-4.1787	0.1946	178	0.152	3363	X-RAY DIFFRACTION	100
4.1787-4.5011	0.198	172	0.1524	3355	X-RAY DIFFRACTION	100
4.5011-4.9537	0.1987	170	0.1505	3411	X-RAY DIFFRACTION	100
4.9537-5.6696	0.2017	178	0.168	3389	X-RAY DIFFRACTION	100
5.6696-7.1396	0.2271	175	0.1873	3424	X-RAY DIFFRACTION	100
7.1396-49.1467	0.1758	179	0.1695	3357	X-RAY DIFFRACTION	99

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	0.5571	-0.186	0.2295	1.078	-0.1876	0.1157	0.2093	0.5859	0.0121	-0.4803	-0.3709	0.0951	-0.3735	-0.5575	-0.2407	0.5922	0.3471	-0.0873	0.6663	-0.0714	0.3215	25.3279	62.1784	82.4036
2	0.9897	-0.1857	0.2692	1.0429	-0.3416	0.2567	0.0414	0.4164	-0.0272	-0.4185	-0.1336	-0.3411	0.0206	-0.0077	-0.297	0.3128	0.0868	-0.0623	0.507	-0.1153	0.3498	35.6818	51.3392	82.9168
3	0.9011	0.2997	0.0932	0.8654	0.1713	0.0516	0.3734	0.0983	-0.141	0.1285	-0.4589	0.1282	-0.2307	-0.443	-0.0854	0.1062	0.2831	-0.0368	0.2449	-0.0624	0.2377	23.6622	58.7406	101.1172
4	0.1101	0.2092	0.0222	0.7109	0.2324	0.1322	0.0109	0.2536	-0.3395	0.1468	-0.2049	0.3409	0.1593	-0.6299	-1.058	0.1215	0.0461	-0.165	0.5396	-0.2284	0.312	20.4221	45.633	97.9951
5	0.0673	0.0551	-0.0481	0.0362	-0.0304	0.0525	0.1798	-0.0755	-0.2316	-0.0024	-0.2572	-0.0474	0.0818	-0.2901	-0	0.2933	0.0592	-0.0542	0.3715	-0.0603	0.4066	34.5587	51.8452	98.2934
6	0.1828	0.3589	0.1801	1.5404	0.2697	0.2457	0.1626	0.0807	-0.2116	0.1694	-0.1704	0.2549	0.1161	-0.2512	0.0896	0.1519	0.0387	-0.0478	0.3882	-0.091	0.3593	18.9588	50.5365	108.6396
7	0.2723	-0.1794	-0.1081	0.5655	0.4761	0.4152	-0.1617	0.048	-0.6903	0.2489	-0.2948	0.3423	0.2689	-0.4312	-0.2456	0.3614	-0.1251	0.0372	0.318	-0.0649	0.5282	16.5886	40.4506	116.4526
8	0.5505	0.4107	0.0661	0.6874	-0.1555	0.1292	0.0527	0.075	-0.353	0.4254	-0.0235	-0.2184	0.0919	0.1918	-0.0367	0.2667	0.0068	-0.0473	0.202	-0.0117	0.3088	30.9033	51.2755	119.609
9	0.0357	-0.028	0.0182	0.0165	-0.0175	0.0827	0.1266	0.2742	-0.5808	-0.5508	0.1025	0.1799	0.5549	-0.0858	0.0014	0.552	-0.0111	-0.0287	0.4592	-0.0184	0.5125	11.1516	91.0838	147.7942
10	0.0045	0.0231	-0.0147	0.0887	0.0343	0.1301	0.0026	-0.3665	-0.5479	0.0903	-0.0529	-0.3791	0.8488	0.4924	-0.0001	0.5866	0.0894	-0.034	0.5827	0.1216	0.6718	19.581	87.0661	155.9788
11	0.2678	-0.1657	-0.1518	0.3437	0.1327	0.2301	-0.0327	-0.123	0.017	0.0595	-0.0194	-0.1498	0.0148	0.3456	-0	0.2656	-0.0131	-0.0187	0.4441	0.0376	0.3647	17.4108	100.4086	157.3126
12	0.4187	0.3036	0.0861	0.3713	0.2235	0.1628	0.0277	0.179	0.162	0.0282	0.1611	0.2229	-0.2323	0.17	0	0.3529	-0.0214	0.0236	0.387	0.0054	0.3296	8.8733	120.1538	149.7132
13	0.0606	-0.1523	-0.0714	0.3251	0.1712	0.325	0.0392	-0.0418	0.2514	0.2289	0.2183	0.2568	-0.2358	0.1465	0.0001	0.297	0.0175	0.0313	0.4879	0.0355	0.3701	9.8781	104.3706	158.5685
14	0.0636	0.0164	0.0135	0.0748	0.0304	0.0096	0.0693	-0.1534	0.1206	0.3889	0.0654	0.4306	-0.2026	-0.036	-0	0.3356	-0.0101	0.0722	0.416	0.0259	0.3766	4.0061	119.3771	153.4551
15	0.3597	-0.3052	0.5552	0.3125	-0.5161	0.9159	0.2996	-0.3666	0.362	0.1808	0.2033	0.2388	-0.2959	-0.3531	0.0723	0.5995	0.0321	0.1761	0.4507	-0.0539	0.463	1.7691	129.863	161.5401
16	0.0292	0.0142	0.0412	0.049	0.0776	0.1244	-0.1243	-0.0438	0.0959	0.2251	0.2012	-0.102	-0.2931	-0.0088	-0	0.5009	-0.0525	0.0574	0.403	-0.0923	0.3602	12.4361	127.1081	158.5451
17	0.029	0.0336	0.0076	0.0445	0.0257	0.0354	0.3535	-0.2674	0.3217	-0.3069	0.0657	-0.1968	-0.3643	0.3407	0.0001	0.5664	-0.0786	0.05	0.4574	-0.0136	0.5374	19.0035	132.9073	141.4475
18	0.466	0.2686	-0.43	0.3064	-0.2597	0.4002	0.2026	0.2772	0.3515	0.0211	0.2254	0.6517	-0.4596	-0.159	0.0857	0.6165	0.0407	0.026	0.427	0.1952	0.6281	1.9124	134.8968	121.0484
19	0.0617	-0.0642	-0.1213	0.0866	0.1295	0.213	0.2377	0.1468	0.3377	0.0861	0.0582	-0.0729	-0.2324	0.1097	0.0187	0.6526	-0.146	0.0438	0.345	0.0543	0.3813	16.8874	136.8883	118.8667
20	0.315	0.1058	-0.1003	0.2581	-0.3086	0.3586	-0.0235	0.0347	0.0392	-0.2493	0.0497	-0.0642	0.0127	0.1511	0	0.5027	-0.0393	0.0435	0.4414	0.0337	0.4643	18.3015	116.227	126.7608
21	0.5319	0.1467	-0.3097	0.257	-0.3154	0.368	0.0336	0.0601	0.0627	-0.3779	-0.0631	-0.1093	0.1514	0.2557	0	0.718	-0.0576	0.0122	0.3606	0.0507	0.4049	16.8835	121.3743	118.2147
22	0.3338	0.1928	0.1025	0.4319	0.188	0.1273	-0.001	0.0274	-0.1583	-0.3635	0.065	-0.4878	-0.1045	0.7581	0.0034	0.4016	-0.0396	0.1395	0.5616	-0.0062	0.4625	31.8684	110.4111	129.7385
23	1.0922	-0.1618	0.6611	0.4879	-0.0238	0.9626	-0.0117	-0.4576	0.0917	0.5398	-0.0364	0.2326	-0.1039	-0.5268	-0.009	0.4988	0.0506	0.0248	0.3428	-0.0319	0.324	22.3107	79.6072	131.3747
24	0.8975	-0.2619	-0.1608	1.2274	0.0421	1.0347	0.1301	-0.0147	0.0828	0.0365	-0.1084	-0.1363	-0.4171	0.1366	0	0.3463	-0.0419	0.0014	0.2344	0.0254	0.2937	38.0806	78.8999	110.6257

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 17 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 143 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 144 through 188 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 189 through 210 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 211 through 246 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 247 through 264 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 265 through 303 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 17 through 38 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 39 through 69 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 70 through 115 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 116 through 162 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 163 through 210 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 211 through 246 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 247 through 263 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 264 through 286 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 287 through 304 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 15 through 68 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 69 through 96 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 97 through 162 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 163 through 228 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 229 through 304 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 15 through 96 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 97 through 304 )

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Movie

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Structure viewers

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Validation report

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Assembly

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi