PDB-4y1o: Oceanobacillus iheyensis group II intron domain 1

ID or keywords:

Entry

Database: PDB / ID: 4y1o

Title

Oceanobacillus iheyensis group II intron domain 1

Components

group II intron, domain 1

Keywords

RNA /

TRANSFERASE /

group II intron /

domain 1

Function / homology

: /

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

Function and homology information

Biological species

Oceanobacillus iheyensis HTE831 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.95 Å

Authors

Zhao, C. / Rajashankar, K.R. / Marcia, M. / Pyle, A.M.

Citation

Journal: Nat.Chem.Biol. / Year: 2015
Title: Crystal structure of group II intron domain 1 reveals a template for RNA assembly.
Authors: Zhao, C. / Rajashankar, K.R. / Marcia, M. / Pyle, A.M.

History

Deposition	Feb 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Database references
Revision 1.2	Nov 25, 2015	Group: Other
Revision 1.3	Dec 2, 2015	Group: Database references
Revision 1.4	Feb 28, 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_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4y1o.cif.gz	574.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4y1o.ent.gz	468.7 KB	Display	PDB format
PDBx/mmJSON format	4y1o.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/y1/4y1o ftp://data.pdbj.org/pub/pdb/validation_reports/y1/4y1o	HTTPS FTP

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Related structure data

Related structure data	4y1nC C: citing same article (ref.)
Similar structure data	4y1n-2 4y1n-1 5iud-2 5l6h-1 5iud-3 6rs1-d 6sj7-d 3jbz-d 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 - 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) #65 - May 2005 Self-splicing RNA similarity (3) #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) #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)
#65 - May 2005
Self-splicing RNA
similarity (3)
#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)
#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, domain 1

B: group II intron, domain 1

hetero molecules

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

1

A: group II intron, domain 1

hetero molecules

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

2

B: group II intron, domain 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.345, 132.250, 84.561
Angle α, β, γ (deg.)	90.00, 91.87, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: RNA chain	group II intron, domain 1 / Mass: 89198.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis HTE831 (bacteria) / References: GenBank: 42632302
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.64 Å³/Da / Density % sol: 53.45 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 80 mM NaCl, 24 mM KCl, 5 mM MgCl2, 40 mM NaCacodylate, 17% MPD, 8 mM spermine-4HCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.95→40.25 Å / Num. obs: 75788 / % possible obs: 98.67 % / Redundancy: 6.8 % / B_iso Wilson estimate: 91.6 Å² / Net I/σ(I): 19.31
Reflection shell	Resolution: 2.95→3.06 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.65 / % possible all: 94.95

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS	January 10, 2014	data reduction
XDS	January 10, 2014	data scaling
PHASER	2.5.2	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: model from an isomorphous crystal

Resolution: 2.95→40.25 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0.37 / Phase error: 29.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2238	3815	5.03 %
R_work	0.1787	-	-
obs	0.1811	75788	98.58 %

Solvent computation

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

Displacement parameters

B_iso mean: 107.383 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→40.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	11044	21	2	11067

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	12367
X-RAY DIFFRACTION	f_angle_d	1.099	19260
X-RAY DIFFRACTION	f_dihedral_angle_d	14.939	6129
X-RAY DIFFRACTION	f_chiral_restr	0.046	2570
X-RAY DIFFRACTION	f_plane_restr	0.007	514

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 (%)
2.9501-2.9874	0.506	127	0.4563	2393	X-RAY DIFFRACTION	90
2.9874-3.0267	0.4116	119	0.385	2667	X-RAY DIFFRACTION	95
3.0267-3.0682	0.4304	143	0.3281	2565	X-RAY DIFFRACTION	98
3.0682-3.112	0.3505	138	0.2779	2739	X-RAY DIFFRACTION	99
3.112-3.1584	0.2993	133	0.2405	2681	X-RAY DIFFRACTION	99
3.1584-3.2078	0.2999	142	0.2222	2698	X-RAY DIFFRACTION	99
3.2078-3.2603	0.2683	157	0.2195	2681	X-RAY DIFFRACTION	99
3.2603-3.3165	0.2867	131	0.218	2583	X-RAY DIFFRACTION	98
3.3165-3.3768	0.3499	165	0.2202	2685	X-RAY DIFFRACTION	98
3.3768-3.4417	0.2545	131	0.2215	2622	X-RAY DIFFRACTION	99
3.4417-3.5119	0.2687	127	0.2327	2787	X-RAY DIFFRACTION	100
3.5119-3.5883	0.2904	128	0.1969	2668	X-RAY DIFFRACTION	100
3.5883-3.6717	0.2838	136	0.2037	2751	X-RAY DIFFRACTION	99
3.6717-3.7634	0.2466	131	0.1858	2650	X-RAY DIFFRACTION	100
3.7634-3.8651	0.2577	142	0.173	2693	X-RAY DIFFRACTION	100
3.8651-3.9787	0.2455	145	0.1866	2667	X-RAY DIFFRACTION	99
3.9787-4.107	0.2483	145	0.1739	2626	X-RAY DIFFRACTION	98
4.107-4.2537	0.2216	148	0.1647	2733	X-RAY DIFFRACTION	99
4.2537-4.4238	0.207	124	0.1687	2690	X-RAY DIFFRACTION	100
4.4238-4.6249	0.2386	156	0.1605	2692	X-RAY DIFFRACTION	100
4.6249-4.8683	0.2172	149	0.16	2701	X-RAY DIFFRACTION	100
4.8683-5.1727	0.1793	159	0.148	2654	X-RAY DIFFRACTION	99
5.1727-5.5712	0.1931	138	0.132	2667	X-RAY DIFFRACTION	98
5.5712-6.1301	0.222	133	0.14	2702	X-RAY DIFFRACTION	100
6.1301-7.013	0.1904	162	0.1596	2683	X-RAY DIFFRACTION	100
7.013-8.8204	0.2102	144	0.1611	2651	X-RAY DIFFRACTION	98
8.8204-40.2568	0.1673	162	0.1753	2644	X-RAY DIFFRACTION	98

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	1.4402	1.0518	-0.5452	1.0632	-0.094	1.2883	-0.0441	0.127	0.4119	-0.7457	-0.153	0.0426	0.5284	0.2029	-0.0518	0.2646	0.056	-0.1672	0.4963	-0.0115	0.4386	4.4065	-23.737	-42.9699
2	-0.4358	0.1016	-0.6669	0.0698	-0.2163	-0.0306	0.2523	0.0536	0.3795	-0.1561	0.2689	0.6182	0.1189	0.1687	0.0065	0.8859	-0.3117	-0.1431	0.6983	0.0759	0.7363	-11.0006	-53.1482	-24.4111
3	-0.2924	-0.0485	0.3268	0.1287	-0.1148	0.3392	-0.0347	0.1415	-0.1556	0.6047	0.2296	-0.0716	0.4646	0.1628	-0.0104	0.7622	-0.0069	0.0107	0.5	-0.0558	0.4822	5.9908	-20.5145	-14.3484
4	-0.2534	0.6013	0.7284	0.6337	1.0578	0.6721	-0.0865	-0.1291	0.1206	0.3165	-0.19	0.4596	0.3338	-0.2314	-0.008	0.5517	-0.0487	0.129	0.6693	-0.0417	0.7463	-11.4316	-7.1282	-22.4989
5	0.6568	0.0314	0.3787	0.0284	0.0473	0.3125	-0.485	-0.9188	0.3768	0.878	-0.7238	0.0578	0.3495	-0.3845	-0.0921	1.2543	-0.1296	0.397	1.0511	-0.1822	1.2929	-19.137	-1.1291	-12.0128
6	0.0701	-0.1888	0.1326	0.0046	-0.1875	-0.092	0.2038	-0.0838	0.0659	0.1103	-0.1834	0.0268	0.0193	0.0537	0.0001	0.7736	-0.0565	0.0829	0.6023	-0.058	0.6371	10.6394	-32.7339	-22.0063
7	1.2992	-0.4199	-0.5454	0.686	-0.3375	2.2097	-0.6896	-0.3508	-0.1656	0.6749	0.4841	0.101	0.3773	0.2094	-0.0116	0.5869	0.0518	-0.0886	0.4948	0.006	0.4691	-29.484	-39.555	-47.8353
8	0.1331	-0.0155	-0.2565	0.0228	-0.0434	0.0415	-0.1179	-0.2607	0.3837	-0.7178	-0.4883	-0.3679	-0.1317	-0.1305	-0.0106	1.0101	-0.1521	0.0314	1.0976	-0.1281	1.4807	3.3561	-36.9589	-67.5647
9	0.9223	-1.5488	-0.8527	-0.2749	0.1805	0.1023	-0.0979	0.0613	0.2993	0.0371	0.1108	0.0443	0.0203	0.1499	0.0019	0.4733	-0.1373	-0.1365	0.7044	-0.0724	0.7984	-10.1163	-44.5796	-65.8141
10	1.2229	-0.5857	0.2492	0.0183	0.3062	0.7918	0.0034	0.3464	0.1105	-0.0913	-0.1083	-0.1184	-0.0883	0.2318	-0.0001	0.6076	-0.0118	0.0679	0.595	0.0916	0.523	-38.4796	-28.4117	-74.7005
11	0.6211	-0.8155	0.2606	-0.0189	-0.1948	0.4948	-0.5277	-0.0145	0.0731	0.0834	0.5647	0.3116	0.2583	0.1503	0.0146	0.7238	0.0702	0.0064	0.4837	0.0226	0.6628	-11.8735	-59.6919	-65.7022

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 115 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 116 through 144 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 145 through 206 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 209 through 223 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 224 through 270 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -4 through 71 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 72 through 86 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 87 through 132 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 133 through 246 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 247 through 270 )

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