PDB-2a2e: Crystal structure of the RNA subunit of Ribonuclease P. Bacterial...

ID or keywords:

Entry

Database: PDB / ID: 2a2e

Title

Crystal structure of the RNA subunit of Ribonuclease P. Bacterial A-type.

Components

RNA subunit of RNase P

Keywords

RNA /

rnase p / ribonuclease p rna / p rna /

ribozyme /

trna / pre-trna /

Thermotoga maritima / tetraloop-receptor / T-loop / coaxial helices / ribose zippers

Function / homology

OSMIUM ION /

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

Function and homology information

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 3.85 Å

Authors

Torres-Larios, A. / Swinger, K.K. / Krasilnikov, A.S. / Pan, T. / Mondragon, A.

Citation

Journal: Nature / Year: 2005
Title: Crystal structure of the RNA component of bacterial ribonuclease P.
Authors: Torres-Larios, A. / Swinger, K.K. / Krasilnikov, A.S. / Pan, T. / Mondragon, A.

History

Deposition	Jun 22, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 6, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 28, 2011	Group: Advisory
Revision 1.4	Jan 22, 2020	Group: Advisory / Derived calculations Category: database_PDB_caveat / ndb_struct_conf_na ...database_PDB_caveat / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.5	Jul 28, 2021	Group: Derived calculations / Refinement description / Category: refine / refine_ls_shell / struct_site Item: _refine.ls_percent_reflns_obs / _refine_ls_shell.percent_reflns_obs ..._refine.ls_percent_reflns_obs / _refine_ls_shell.percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6	Aug 23, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ...

Remark 999

SEQUENCE SEE REMARK 3, OTHER REFINEMENT REMARKS, FOR DETAILS REGARDING SOME LONG P-O3* BOND DISTANCES.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2a2e.cif.gz	151.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2a2e.ent.gz	105.9 KB	Display	PDB format
PDBx/mmJSON format	2a2e.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/a2/2a2e ftp://data.pdbj.org/pub/pdb/validation_reports/a2/2a2e	HTTPS FTP

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Related structure data

Related structure data	1u9sS 1nbs S: Starting model for refinement
Similar structure data	4yg8-d 5v3i-d 4r4p-d 4liq-d 1olm-d 4r4v-d 4n0u-d 6wrw-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) #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: RNA subunit of RNase P

hetero molecules

113 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	179.277, 85.231, 101.912
Angle α, β, γ (deg.)	90.00, 96.83, 90.00
Int Tables number	5
Space group name H-M	C121

#1: RNA chain	RNA subunit of RNase P / Mass: 109668.031 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in Thermotoga maritima. The RNA was prepared by in vitro transcrption.
#2: Chemical	ChemComp-OS / OSMIUM ION / Osmium Mass: 190.230 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Os

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal	Density Matthews: 3.4 Å³/Da / Density % sol: 60 %
Crystal grow	Temperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% MPD, 200 mM KCl, 5 mM SrCl2, 50 mM MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1
4	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength
SYNCHROTRON	APS	5ID-B	1	1.13974
SYNCHROTRON	APS	5ID-B	2	1.14079
SYNCHROTRON	APS	5ID-B	3	1.105
SYNCHROTRON	APS	5ID-B	4	1.13974

Detector

Type	ID	Detector	Date	Details
MARRESEARCH	1	CCD	Nov 11, 2004	mirrors
MARRESEARCH	2	CCD	Nov 11, 2004	mirrors
MARRESEARCH	3	CCD	Nov 11, 2004	mirrors
marccd	4	CCD	Nov 11, 2004	mirrors

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SI mirrors	SINGLE WAVELENGTH	M	x-ray	1
2	SI mirrors	SINGLE WAVELENGTH	M	x-ray	1
3	SI mirrors	SINGLE WAVELENGTH	M	x-ray	1
4	SI mirrors	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.13974	1
2	1.14079	1
3	1.105	1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	% possible obs
4.2	1	7.9	12565	0.084	0.084	4.05	19.91	98.7
4.2	2	7.9	12565	0.084	0.084	4.05	19.91	98.7
4.2	3	7.9	12565	0.084	0.084	4.05	19.91	98.7
2.7	4	11.5	13927	0.06	0.06	3.85	21.05	97.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
15.49	19.91	52.9	1	0.034	0.034	3.8
10.95	15.49	99.4	1	0.03	0.03	4.1
8.94	10.95	98.8	1	0.04	0.04	4.1
7.75	8.94	100	1	0.043	0.043	4.3
6.93	7.75	100	1	0.05	0.05	4.5
6.32	6.93	99.9	1	0.064	0.064	4.4
5.86	6.32	100	1	0.081	0.081	4.5
5.48	5.86	100	1	0.097	0.097	4.4
5.16	5.48	99.8	1	0.115	0.115	4.4
4.9	5.16	99.8	1	0.15	0.15	4.3
4.67	4.9	99.9	1	0.183	0.183	4.3
4.47	4.67	100	1	0.222	0.222	4.2
4.3	4.47	99.9	1	0.241	0.241	4.2
4.14	4.3	99.7	1	0.275	0.275	3.9
4.05	4.14	95	1	0.286	0.286	3.8
15.49	19.91	52.9	2	0.034	0.034	3.8
10.95	15.49	99.4	2	0.03	0.03	4.1
8.94	10.95	98.8	2	0.04	0.04	4.1
7.75	8.94	100	2	0.043	0.043	4.3
6.93	7.75	100	2	0.05	0.05	4.5
6.32	6.93	99.9	2	0.064	0.064	4.4
5.86	6.32	100	2	0.081	0.081	4.5
5.48	5.86	100	2	0.097	0.097	4.4
5.16	5.48	99.8	2	0.115	0.115	4.4
4.9	5.16	99.8	2	0.15	0.15	4.3
4.67	4.9	99.9	2	0.183	0.183	4.3
4.47	4.67	100	2	0.222	0.222	4.2
4.3	4.47	99.9	2	0.241	0.241	4.2
4.14	4.3	99.7	2	0.275	0.275	3.9
4.05	4.14	95	2	0.286	0.286	3.8
15.49	19.91	52.9	3	0.034	0.034	3.8
10.95	15.49	99.4	3	0.03	0.03	4.1
8.94	10.95	98.8	3	0.04	0.04	4.1
7.75	8.94	100	3	0.043	0.043	4.3
6.93	7.75	100	3	0.05	0.05	4.5
6.32	6.93	99.9	3	0.064	0.064	4.4
5.86	6.32	100	3	0.081	0.081	4.5
5.48	5.86	100	3	0.097	0.097	4.4
5.16	5.48	99.8	3	0.115	0.115	4.4
4.9	5.16	99.8	3	0.15	0.15	4.3
4.67	4.9	99.9	3	0.183	0.183	4.3
4.47	4.67	100	3	0.222	0.222	4.2
4.3	4.47	99.9	3	0.241	0.241	4.2
4.14	4.3	99.7	3	0.275	0.275	3.9
4.05	4.14	95	3	0.286	0.286	3.8
17.22	21.05	12.9	4	0.043	0.043	1.3
12.17	17.22	82.6	4	0.022	0.022	2.3
9.94	12.17	98.1	4	0.024	0.024	2.6
8.61	9.94	97.5	4	0.037	0.037	2.7
7.7	8.61	98.2	4	0.032	0.032	2.7
7.03	7.7	98.2	4	0.033	0.033	2.8
6.51	7.03	98.5	4	0.038	0.038	2.8
6.09	6.51	98.4	4	0.042	0.042	2.7
5.74	6.09	98.7	4	0.046	0.046	2.7
5.44	5.74	98.3	4	0.05	0.05	2.7
5.19	5.44	98.9	4	0.059	0.059	2.7
4.97	5.19	99	4	0.073	0.073	2.7
4.78	4.97	98.3	4	0.088	0.088	2.7
4.6	4.78	99	4	0.101	0.101	2.7
4.45	4.6	98.5	4	0.123	0.123	2.7
4.3	4.45	99	4	0.141	0.141	2.7
4.18	4.3	98.4	4	0.171	0.171	2.6
4.06	4.18	98	4	0.176	0.176	2.6
3.95	4.06	98	4	0.195	0.195	2.6
3.85	3.95	98.9	4	0.231	0.231	2.6

Reflection

Resolution: 3.85→21.05 Å / Num. all: 14328 / Num. obs: 13927 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / R_merge(I) obs: 0.06 / R_sym value: 0.06 / Net I/σ(I): 11.5

Reflection shell

Resolution: 3.85→3.95 Å / % possible obs: 98.9 % / Redundancy: 2.6 % / R_merge(I) obs: 0.231 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 1046 / Num. unique all: 1046 / R_sym value: 0.231 / % possible all: 98.9

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Phasing

Phasing

Method:

SIRAS

Phasing set

ID
1
2
3
4

Phasing MR

	Highest resolution	Lowest resolution
Translation	4.5 Å	11.998 Å

Phasing MIR

Resolution: 3.85→14.98 Å / FOM acentric: 0.45 / FOM centric: 0.385 / Reflection acentric: 12936 / Reflection centric: 745

Phasing MIR der

Native set-ID: 1 / Resolution: 3.85→14.98 Å

ID	R cullis acentric	R cullis centric	Der set-ID	Reflection acentric	Reflection centric
ISO_1	0	0	1	11795	682
ISO_2	0.685	0.752	2	11751	633
ISO_3	0.635	0.751	3	11499	608
ISO_4	0.889	0.876	4	11403	619

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
9.01	14.98	ISO_1	0	0	739	87
7.04	9.01	ISO_1	0	0	1120	78
5.97	7.04	ISO_1	0	0	1433	92
5.27	5.97	ISO_1	0	0	1633	101
4.78	5.27	ISO_1	0	0	1842	97
4.4	4.78	ISO_1	0	0	2027	101
4.1	4.4	ISO_1	0	0	2148	89
3.85	4.1	ISO_1	0	0	853	37
9.01	14.98	ISO_2	0.681	0.722	739	86
7.04	9.01	ISO_2	0.744	0.769	1120	76
5.97	7.04	ISO_2	0.731	0.755	1433	91
5.27	5.97	ISO_2	0.672	0.746	1633	98
4.78	5.27	ISO_2	0.695	0.736	1839	84
4.4	4.78	ISO_2	0.668	0.762	2027	95
4.1	4.4	ISO_2	0.642	0.735	2140	73
3.85	4.1	ISO_2	0.714	0.802	820	30
9.01	14.98	ISO_3	0.569	0.683	699	76
7.04	9.01	ISO_3	0.648	0.905	1097	71
5.97	7.04	ISO_3	0.679	0.849	1411	84
5.27	5.97	ISO_3	0.674	0.757	1608	94
4.78	5.27	ISO_3	0.687	0.729	1807	85
4.4	4.78	ISO_3	0.664	0.738	1988	93
4.1	4.4	ISO_3	0.621	0.839	2072	75
3.85	4.1	ISO_3	0.66	0.777	817	30
9.01	14.98	ISO_4	0.811	0.883	734	86
7.04	9.01	ISO_4	0.813	0.868	1120	78
5.97	7.04	ISO_4	0.817	0.84	1432	91
5.27	5.97	ISO_4	0.807	0.796	1632	97
4.78	5.27	ISO_4	0.867	0.845	1839	83
4.4	4.78	ISO_4	0.905	0.874	2025	90
4.1	4.4	ISO_4	1.003	0.941	2140	73
3.85	4.1	ISO_4	1.05	0.947	481	21

Phasing MIR shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
9.01-14.98	0.874	0.688	742	87
7.04-9.01	0.792	0.627	1124	78
5.97-7.04	0.68	0.506	1433	92
5.27-5.97	0.563	0.424	1633	103
4.78-5.27	0.442	0.331	1842	99
4.4-4.78	0.365	0.268	2027	101
4.1-4.4	0.294	0.229	2150	91
3.85-4.1	0.1	0.077	1985	94

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Processing

Software

Name	Version	Classification
SCALA		data scaling
PHASER		phasing
SHARP		phasing
SOLOMON		phasing
CNS		refinement
PDB_EXTRACT	1.601	data extraction
CCP4	(SCALA)	data scaling

Refinement

Starting model: PDB ENTRY 1U9S

1u9s

Resolution: 3.85→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: maximum likelihood
Details: No bulk solvent correction applied. Only the phosphate backbone was traced (phosphate atom only) for nucleotides 39, 45-48, 52, 62-63, 68, 207, 212-214, 262-267, 288-297 and 305-314. There ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3617	602	-	RANDOM
R_work	0.3441	-	-	-
all	0.363	12980	-	-
obs	0.356	12652	97.5 %	-

Displacement parameters

B_iso mean: 81.165 Å²

Refinement step

Cycle: LAST / Resolution: 3.85→8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	5758	17	0	5775

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	c_bond_d	0.009
X-RAY DIFFRACTION	c_angle_deg	1.87
X-RAY DIFFRACTION	c_improper_angle_d	2.14
X-RAY DIFFRACTION	c_dihedral_angle_d	18

LS refinement shell

Resolution: 3.85→4.01 Å / R_factor R_free error: 0.051

	R_factor	Num. reflection	% reflection
R_free	0.431	55	5.7 %
R_work	0.377	903	-
obs	-	-	59 %

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