PDB-3g78: Insight into group II intron catalysis from revised crystal structure

ID or keywords:

Entry

Database: PDB / ID: 3g78

Title

Insight into group II intron catalysis from revised crystal structure

Components

Group II intron
Ligated EXON product

Keywords

RNA / revised crystal structure / revision

Function / homology

: /

RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

Oceanobacillus iheyensis (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 2.8 Å

Authors

Wang, J.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for exon recognition by a group II intron.
Authors: Toor, N. / Rajashankar, K. / Keating, K.S. / Pyle, A.M.

History

Deposition	Feb 9, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 16, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Sep 21, 2011	Group: Other
Revision 1.3	Oct 5, 2011	Group: Other
Revision 1.4	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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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

Remark 0

THIS ENTRY 3G78 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA DETERMINED BY ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3g78.cif.gz	248.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3g78.ent.gz	187.4 KB	Display	PDB format
PDBx/mmJSON format	3g78.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g7/3g78 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g78	HTTPS FTP

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Related structure data

Related structure data	3bwp 3eoh
Similar structure data	4far-d 4fau-d 4faq-d 4e8r-d 4e8v-d 4e8n-d 3igi-d 4ds6-d 6t3n-d 4e8q-d 4fax-d 4faw-d 3eog-d 3eoh-d 4fb0-d 4e8k-d 6t3k-d 4e8t-d 6t3r-d 6t3s-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #10 - Oct 2000 Ribosome similarity (2) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (2) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #98 - Feb 2008 Small Interfering RNA similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #161 - May 2013 Ricin similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #227 - Nov 2018 Telomerase similarity (2) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#260 - Aug 2021
Ribonuclease P
similarity (2)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#245 - May 2020
Spliceosomes
similarity (2)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Group II intron

Z: Ligated EXON product

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	89.109, 94.970, 225.998
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: RNA chain	Group II intron / Mass: 133652.156 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA was pepared by in vitro transcription by T7 RNA polymerase Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: RNA chain	Ligated EXON product Mass: 2772.615 Da / Num. of mol.: 1 / Fragment: unknown exon product / Source method: obtained synthetically
#3: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	... ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: K
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 64.9 % Description: AUTHOR USED THE SF DATA FROM THE PDB ENTRY 3BWP.

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Data collection

Radiation	Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.8→40 Å / Num. all: 47850 / Num. obs: 47323 / % possible obs: 98.9 % / Observed criterion σ(F): 0.75 / Observed criterion σ(I): 0.37 / Redundancy: 6.3 % / R_merge(I) obs: 0.072 / Net I/σ(I): 20.71
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 0.37 / Num. unique all: 4323 / % possible all: 92.1

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MLPHARE		phasing
REFMAC	5.4.0077	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Resolution: 2.8→39.29 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.926 / SU B: 30.309 / SU ML: 0.245 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.597 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22661	2346	5 %	RANDOM
R_work	0.19443	-	-	-
obs	0.19605	44197	97.2 %	-

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: 20.004 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.91 Å²	0 Å²	0 Å²
2-	-	3.53 Å²	0 Å²
3-	-	-	0.39 Å²

Refine analyze

Luzzati coordinate error free: 0.295 Å

Refinement step

Cycle: LAST / Resolution: 2.8→39.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	8545	77	435	9057

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.021	9574
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.21	3	14933
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	1988
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4173
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it	0.591	3	9574
X-RAY DIFFRACTION	r_scangle_it	1.022	4.5	14933
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.804→2.877 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.697	136	-
R_work	0.627	2424	-
obs	-	-	73.27 %

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	9.3308	1.9523	3.2723	14.6901	4.904	3.2619	-0.1334	-0.5169	-0.2816	0.9406	0.1468	0.4749	0.3624	-0.3367	-0.0133	0.5719	0.0033	-0.0878	0.4135	0.011	0.3162	25.191	68.127	141.248
2	0.7253	-1.2291	0.8863	3.5298	-2.499	2.1987	0.0032	0.4317	0.3263	0.0205	-0.6277	-1.3163	-0.0537	0.7732	0.6245	0.5585	-0.0055	-0.0122	0.452	0.2523	0.8494	38.237	87.15	122.887
3	5.6571	0.9798	0.1456	0.4331	0.3372	0.3732	-0.3964	0.6638	-0.0543	-0.2804	0.2918	-0.1726	-0.188	0.1816	0.1047	0.6255	-0.1164	-0.0439	0.2573	0.1055	0.5084	9.275	108.021	106.489
4	2.8572	0.5809	2.0736	3.0253	2.2383	5.8417	-0.1996	-0.8885	0.0176	0.3338	-0.2029	0.8495	0.6215	-2.1752	0.4026	0.5688	-0.1127	0.0869	0.8175	0.0224	0.5987	-21.258	99.435	117.708
5	0.5854	-0.9824	0.3629	5.3659	-1.809	1.5712	0.1434	0.0254	0.0401	-0.4963	-0.0788	0.0888	0.2966	0.2102	-0.0647	0.5673	0.0804	-0.0608	0.0619	-0.0216	0.4376	19.208	81.476	121.103
6	4.8442	-4.418	1.1014	6.8266	-1.5964	2.6471	-0.0488	0.0168	-0.2763	0.4539	-0.124	0.898	0.1403	-0.1567	0.1729	0.6276	0.1348	-0.0309	0.0726	-0.0153	0.5157	26.232	48.516	131.601
7	1.2914	0.7069	1.3595	2.1395	-1.5834	4.5227	-0.1429	-0.296	0.4369	0.5963	0.0871	-0.427	-0.8716	0.2316	0.0559	0.8309	0.0286	-0.101	0.298	-0.0688	0.4931	16.177	109.02	132.505
8	1.7743	-2.6449	-1.4209	4.3269	0.7986	5.6706	-0.227	-0.7235	0.7937	1.5282	0.2699	-0.1608	-0.283	-0.3259	-0.0428	1.4677	0.2761	-0.2747	0.4536	-0.2941	0.3129	19.206	93.499	162.398
9	2.3669	0.3124	1.7417	3.0082	-2.0684	3.0619	-0.432	-0.8876	0.7272	1.1033	0.3562	-0.0288	-1.2553	-1.0694	0.0758	1.5267	0.4619	0.0852	0.4718	-0.1716	0.3033	8.326	102.249	158.379
10	3.8535	-1.3444	0.8807	2.4672	-2.3877	10.3822	-0.8675	-1.1634	-0.179	1.1852	1.1182	0.6641	-1.7716	-2.0029	-0.2507	0.9569	0.3719	0.2595	0.9456	0.1066	0.2385	-13.383	98.198	149.477
11	2.1867	-0.678	2.5983	0.9569	-1.8387	6.5075	-0.2096	-0.5204	-0.1141	0.452	0.2974	0.2005	-0.3404	-0.3518	-0.0879	0.5828	0.181	0.0398	0.3068	0.0274	0.403	-2.2	101.72	129.425
12	6.2681	-4.7486	0.8765	6.8892	0.7772	1.7841	-0.1688	-1.0885	-1.2496	0.9536	0.7232	1.4688	0.5186	-0.9991	-0.5544	0.7732	0.0359	0.0147	0.5655	0.2773	0.5649	4.264	80.661	143.111
13	1.242	-2.2518	-0.2085	5.4629	1.2381	0.7404	-0.1637	-0.5371	0.2055	0.573	-0.1029	-0.1663	0.2447	0.0829	0.2665	0.8101	0.1003	-0.2151	0.3032	0.0914	0.4875	40.505	52.48	147.992
14	10.8298	1.6995	-3.9921	8.5137	-2.9378	7.8806	-0.1289	0.0166	0.8946	-0.8056	0.0152	-2.2696	0.0762	2.1668	0.1137	0.4308	-0.0165	-0.2698	1.0106	0.1759	1.5184	65.021	77.176	137.576
15	0.1715	-0.4873	-0.3639	1.442	1.5053	4.6679	0.0129	-0.3703	0.189	0.7845	-0.0367	-0.4325	0.1007	0.6591	0.0239	0.9241	0.0284	-0.3901	0.5378	-0.0673	0.6533	41.686	70.397	161.455
16	10.6862	-1.2378	3.3846	6.0649	3.9294	4.2258	0.1446	-0.5977	-0.4047	-0.0089	0.2522	0.5231	1.2531	-0.7091	-0.3969	0.9556	-0.1349	-0.2053	0.6793	-0.214	0.3668	31.117	80.357	188.499
17	17.5821	-0.8706	-6.7591	12.6674	-2.4977	3.2339	-0.0806	-1.1548	0.9996	0.3224	1.0047	1.6671	0.3342	-0.232	-0.9241	0.7461	-0.056	-0.0465	1.0198	-0.1714	0.5663	20.991	89.307	199.361
18	1.894	-0.9809	1.5906	3.5881	-0.176	5.5875	-0.1046	-0.2215	0.1576	0.6823	0.2077	-0.3985	-0.2654	0.0047	-0.1031	0.7229	0.0679	-0.2154	0.2772	-0.1068	0.3559	23.861	82.64	149.774

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 5
2	X-RAY DIFFRACTION	2	A	6 - 24
3	X-RAY DIFFRACTION	2	A	247 - 266
4	X-RAY DIFFRACTION	3	A	25 - 49
5	X-RAY DIFFRACTION	3	A	59 - 66
6	X-RAY DIFFRACTION	4	A	50 - 58
7	X-RAY DIFFRACTION	4	A	198 - 208
8	X-RAY DIFFRACTION	5	A	67 - 78
9	X-RAY DIFFRACTION	5	A	104 - 121
10	X-RAY DIFFRACTION	6	A	79 - 103
11	X-RAY DIFFRACTION	7	A	122 - 133
12	X-RAY DIFFRACTION	7	A	230 - 246
13	X-RAY DIFFRACTION	8	A	134 - 144
14	X-RAY DIFFRACTION	9	A	145 - 150
15	X-RAY DIFFRACTION	9	A	224 - 229
16	X-RAY DIFFRACTION	10	A	151 - 168
17	X-RAY DIFFRACTION	10	A	209 - 223
18	X-RAY DIFFRACTION	11	A	169 - 178
19	X-RAY DIFFRACTION	11	A	187 - 197
20	X-RAY DIFFRACTION	12	A	179 - 186
21	X-RAY DIFFRACTION	12	A	413 - 414
22	X-RAY DIFFRACTION	12	Z	10 - 12
23	X-RAY DIFFRACTION	13	A	267 - 289
24	X-RAY DIFFRACTION	14	A	304 - 317
25	X-RAY DIFFRACTION	15	A	290 - 303
26	X-RAY DIFFRACTION	15	A	318 - 331
27	X-RAY DIFFRACTION	15	A	351 - 354
28	X-RAY DIFFRACTION	16	A	332 - 336
29	X-RAY DIFFRACTION	16	A	345 - 350
30	X-RAY DIFFRACTION	17	A	337 - 344
31	X-RAY DIFFRACTION	18	A	355 - 390

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Structure viewers

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Viewer log

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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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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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi