PDB-2vrt: Crystal Structure of E. coli RNase E possessing M1 RNA fragments ...

ID or keywords:

Entry

Database: PDB / ID: 2vrt

Title

Crystal Structure of E. coli RNase E possessing M1 RNA fragments - Catalytic Domain

Components

5'-R(*UP*UP)-3'
5'-R(*UP*UP*GP)-3'
RIBONUCLEASE E

Keywords

HYDROLASE / RNA PROCESSING / M1 RNA / RNASE P / NUCLEASE / CYTOPLASM / RNA-BINDING / RNA TURNOVER / ENDONUCLEASE

Function / homology

Function and homology information

regulation of RNA helicase activity / rRNA 5'-end processing / bacterial degradosome / ribonuclease E / ribonuclease E activity / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing ...
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Koslover, D.J. / Callaghan, A.J. / Marcaida, M.J. / Garman, E.F. / Martick, M. / Scott, W.G. / Luisi, B.F.

Citation

Journal: Structure / Year: 2008
Title: The Crystal Structure of the Escherichia Coli Rnase E Apoprotein and a Mechanism for RNA Degradation.
Authors: Koslover, D.J. / Callaghan, A.J. / Marcaida, M.J. / Garman, E.F. / Martick, M. / Scott, W.G. / Luisi, B.F.

History

Deposition	Apr 14, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "DB" IN EACH CHAIN ON SHEET RECORDS ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vrt.cif.gz	668.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2vrt.ent.gz	555.6 KB	Display	PDB format
PDBx/mmJSON format	2vrt.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/vr/2vrt ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrt	HTTPS FTP

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Related structure data

Related structure data	2vmkC 2bx2S 1slj 1smx 1sn8 2c0b 2c4r 2fym S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hsn-d 4u90-d 3wbk-2 2v5d-d 6g0c-d 2ol2-d 5es9-2 4kyd-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) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#253 - Jan 2021 Expressome similarity (4) #255 - Mar 2021 Cisplatin and DNA similarity (3) #86 - Feb 2007 Exosomes similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

A: RIBONUCLEASE E

B: RIBONUCLEASE E

C: RIBONUCLEASE E

D: RIBONUCLEASE E

E: 5'-R(*UP*UP)-3'

F: 5'-R(*UP*UP)-3'

G: 5'-R(*UP*UP*GP)-3'

H: 5'-R(*UP*UP*GP)-3'

hetero molecules

232 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RIBONUCLEASE E

F: 5'-R(*UP*UP)-3'

hetero molecules

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

2

B: RIBONUCLEASE E

G: 5'-R(*UP*UP*GP)-3'

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

3

C: RIBONUCLEASE E

H: 5'-R(*UP*UP*GP)-3'

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

4

D: RIBONUCLEASE E

E: 5'-R(*UP*UP)-3'

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.894, 121.252, 242.228
Angle α, β, γ (deg.)	90.00, 99.47, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 32
2	1	1	1	B	1 - 32
3	1	1	1	C	1 - 32
4	1	1	1	D	1 - 32
1	2	1	1	A	212 - 277
2	2	1	1	B	212 - 277
3	2	1	1	C	212 - 277
4	2	1	1	D	212 - 277
1	1	2	1	A	280 - 393
2	1	2	1	B	280 - 393
3	1	2	1	C	280 - 393
4	1	2	1	D	280 - 393
1	1	3	1	A	40 - 209
2	1	3	1	D	40 - 209
1	1	4	1	B	121 - 209
2	1	4	1	C	121 - 209
1	1	5	1	A	413 - 510
2	1	5	1	B	413 - 510
3	1	5	1	C	413 - 510
4	1	5	1	D	413 - 510

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	RIBONUCLEASE E / RNASE E Mass: 57280.043 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET16B VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: RNA chain	5'-R(UPUP)-3' Mass: 567.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: RNA chain	5'-R(UPUPGP)-3' Mass: 912.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI* (E. coli)
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.67 Å³/Da / Density % sol: 55.5 % / Description: NONE
Crystal grow	pH: 7.5 Details: 10% PEG 4000, 100 MM (NH4)2SO4, AND 100 MM HEPES PH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975
Detector	Type: QUANTUM / Detector: CCD / Date: Mar 19, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.975 Å / Relative weight: 1
Reflection	Resolution: 3.5→79.5 Å / Num. obs: 33891 / % possible obs: 99.9 % / Redundancy: 3.9 % / R_merge(I) obs: 0.12 / Net I/σ(I): 9.6
Reflection shell	Resolution: 3.5→3.69 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
MOLREP		phasing
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BX2

2bx2

Resolution: 3.5→24.98 Å / Cor.coef. F_o:F_c: 0.805 / Cor.coef. F_o:F_c free: 0.768 / SU B: 117.646 / SU ML: 1.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.838 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO OUT OF THE FOUR EXPECTED S1 DOMAINS (RESIDUES 36-118, CHAINS B AND C) ARE MISSING AND PRESUMED TO BE EITHER ABSENT OR DISORDERED IN THE CRYSTAL.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.351	3402	10.1 %	RANDOM
R_work	0.317	-	-	-
obs	0.321	30393	99.9 %	-

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: 108.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.11 Å²	0 Å²	1.73 Å²
2-	-	-0.92 Å²	0 Å²
3-	-	-	1.38 Å²

Refinement step

Cycle: LAST / Resolution: 3.5→24.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12974	210	2	0	13186

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.021	13382
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.134	1.988	18238
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.483	5	1734
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.732	23.879	544
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.144	15	2030
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.753	15	104
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	2200
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10010
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.281	0.2	6242
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	9105
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	475
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	0.334	0.2	48
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.322	0.2	2
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	2.768	1.5	8775
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.008	2	13908
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.097	3	4607
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.513	4.5	4330
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	625	tight positional	0.35	0.05
1	2	B	625	tight positional	0.35	0.05
1	3	C	625	tight positional	0.22	0.05
1	4	D	625	tight positional	0.26	0.05
2	1	A	765	tight positional	0.29	0.05
2	2	B	765	tight positional	0.23	0.05
2	3	C	765	tight positional	0.3	0.05
2	4	D	765	tight positional	0.28	0.05
3	1	A	1110	tight positional	0.3	0.05
4	1	B	523	tight positional	0.54	0.05
5	1	A	597	tight positional	0.36	0.05
5	2	B	597	tight positional	0.28	0.05
5	3	C	597	tight positional	0.25	0.05
5	4	D	597	tight positional	0.21	0.05
1	1	A	625	tight thermal	0.27	0.5
1	2	B	625	tight thermal	0.27	0.5
1	3	C	625	tight thermal	0.25	0.5
1	4	D	625	tight thermal	0.29	0.5
2	1	A	765	tight thermal	0.43	0.5
2	2	B	765	tight thermal	0.48	0.5
2	3	C	765	tight thermal	0.7	0.5
2	4	D	765	tight thermal	0.46	0.5
3	1	A	1110	tight thermal	0.86	0.5
4	1	B	523	tight thermal	3.15	0.5
5	1	A	597	tight thermal	0.25	0.5
5	2	B	597	tight thermal	0.22	0.5
5	3	C	597	tight thermal	0.27	0.5
5	4	D	597	tight thermal	0.23	0.5

LS refinement shell

Resolution: 3.5→3.59 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.395	270
R_work	0.376	2134

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	15.8617	-6.3205	-10.1847	4.3103	1.7585	11.5297	0.7925	-0.062	0.2627	0.1607	-1.5778	-0.1613	0.5704	1.1005	0.7853	-0.5573	-0.0521	-0.7045	0.5095	-0.1327	-0.2643	25.9434	-34.2871	45.2763
2	1.2621	0.5733	-0.2768	1.7288	2.4553	4.5975	-0.2978	-0.493	0.5992	-0.6126	0.3586	-0.5174	-0.0764	-0.2939	-0.0608	0.4208	0.0877	-0.1694	-0.0268	0.0264	0.9012	37.8537	-49.2541	27.0208
3	12.0494	1.581	-2.1627	2.8457	-2.8751	7.9129	0.2881	-0.0158	-0.0453	-0.4628	-0.9237	-1.1121	0.1627	0.8024	0.6356	-0.0548	0.1432	-0.5601	0.1534	-0.0997	0.019	31.7178	-35.987	46.774
4	6.6951	-0.2506	1.1991	6.0143	1.058	6.1177	-0.4927	-0.6572	0.7898	0.566	0.5736	-0.5273	-0.5672	0.7721	-0.0809	-0.5113	0.3809	-0.0803	0.0203	-0.2199	-0.0365	13.4268	-26.5471	26.2503
5	7.1134	-0.945	-0.7971	2.7328	1.1363	7.7355	-0.1295	0.0214	-0.5866	-0.2597	0.1642	0.4605	0.3543	-0.0564	-0.0347	0.0644	-0.0059	-0.0458	0.1769	0.2351	-0.1619	-26.6089	-44.9686	43.7963
6	4.8413	0.949	1.1397	5.3747	-7.6072	12.0861	0.4756	-1.061	0.3302	0.7332	0.0264	-0.77	0.203	-0.2846	-0.502	-0.605	-0.1332	0.0615	0.082	-0.0975	0.1496	-28.1638	-34.7364	21.6933
7	2.7503	-1.8109	-1.1587	7.9798	1.0361	2.6521	0.1134	0.0028	0.1547	-0.0815	-0.2307	0.1996	-0.098	0.1022	0.1173	-0.3269	0.3306	-0.0659	-0.369	0.0777	-0.2171	-26.7803	-10.3305	2.7509
8	4.6319	1.9784	1.4897	2.5861	-2.8038	8.399	0.2387	-0.409	-0.0601	-0.9541	-0.0109	0.5186	0.295	-0.4565	-0.2278	-0.1765	0.0127	0.1419	-0.2268	0.119	0.4143	-33.5062	-32.6901	18.0613
9	6.364	1.713	1.6656	8.8414	1.5588	3.0823	-0.1956	-0.4183	-0.5139	0.1589	-0.1688	0.2882	0.2343	-0.0065	0.3644	-0.3708	0.5413	0.1169	-0.3985	0.2487	-0.3839	-4.1697	-40.7678	17.3735
10	4.4188	3.1553	-0.0055	5.413	-0.8627	5.6002	0.1798	0.2585	0.5341	0.4332	-0.2641	-0.3519	-0.164	-0.2464	0.0843	0.1884	0.3791	-0.1205	0.435	-0.0344	0.031	8.6707	-31.7062	63.1072
11	12.514	5.731	-1.4439	10.0802	3.8561	8.2774	0.1577	1.1774	-0.0495	-2.0301	0.7703	-0.1773	0.4464	-0.4742	-0.928	-0.2201	0.0931	0.1533	-0.1746	-0.1314	0.0146	7.0443	-45.4329	96.6257
12	3.1101	1.6398	0.9014	5.9471	-0.4442	2.3187	0.0604	0.0218	0.0351	0.1059	-0.4352	-0.1896	-0.0974	-0.398	0.3748	-0.1586	0.0347	0.2745	-0.3433	0.1654	-0.1181	6.5332	-21.4293	116.1102
13	4.7603	-2.5738	0.2793	2.7529	-0.6895	7.3236	0.306	-0.0266	0.1184	0.1492	0.3038	-0.8492	0.0009	0.5176	-0.6098	-0.1073	0.0194	0.233	-0.2672	-0.0176	0.3719	12.599	-43.4319	100.2834
14	5.1479	-0.3962	2.2746	5.6402	-0.5965	6.2572	0.1899	0.3163	-0.7271	-0.0145	-0.1305	-0.3987	0.3576	0.0127	-0.0593	-0.3709	-0.075	0.1209	-0.502	-0.0271	-0.3528	-16.5885	-51.3689	101.4972
15	4.6354	-2.2876	0.247	1.4867	1.4388	6.823	-0.1855	-0.3249	0.4388	-0.3352	0.1777	0.7987	-0.1753	-0.2888	0.0078	0.0487	0.1682	0.0892	0.4464	0.2477	0.1719	-32.8574	-35.5515	59.4589
16	10.592	2.0173	-9.2793	1.5606	-5.9144	22.7491	0.2917	-0.3951	0.1892	-1.3167	0.2359	-0.2448	0.399	-0.4745	-0.5275	-0.6524	0.1492	-0.4989	0.3363	0.2317	0.1153	-48.4659	-41.3358	75.3431
17	1.0964	-0.3058	2.1567	1.989	-3.8088	9.6459	0.2728	-0.3454	-0.3951	0.2307	0.1904	0.0643	0.119	-0.2506	-0.4631	0.0264	0.0485	0.1603	0.2227	-0.1156	0.602	-60.0682	-57.8563	95.3674
18	8.7726	0.5764	0.8208	4.3935	0.6343	5.13	0.2772	0.2788	0.3702	-0.4454	-0.4852	1.3538	-0.1833	-0.61	0.2079	-0.2322	0.1884	-0.2113	0.5223	0.0291	0.2758	-54.2782	-43.1744	74.8837
19	4.5753	-3.5254	-0.2984	6.6506	-1.482	6.6289	-0.2039	0.2993	0.9223	-0.1513	0.1872	-0.0227	-1.2355	-0.6901	0.0167	-0.6008	-0.1502	0.1696	-0.0238	0.1907	-0.0874	-34.1212	-36.2125	93.9895
20	0.02	0.3119	-0.0873	4.8909	-1.6618	6.1305	0.2529	0.2408	-0.7897	1.0446	-0.5073	-0.0172	0.2232	-0.2842	0.2544	0.1905	0.1901	-0.0306	0.2774	-0.0667	0.247	4.8603	-49.1216	71.4995

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	C	-6 - 31
2	X-RAY DIFFRACTION	2	C	121 - 209
3	X-RAY DIFFRACTION	3	C	212 - 279
4	X-RAY DIFFRACTION	4	C	280 - 393
5	X-RAY DIFFRACTION	5	C	413 - 510
6	X-RAY DIFFRACTION	6	D	-6 - 31
7	X-RAY DIFFRACTION	7	D	40 - 209
8	X-RAY DIFFRACTION	8	D	212 - 279
9	X-RAY DIFFRACTION	9	D	280 - 393
10	X-RAY DIFFRACTION	10	D	413 - 510
11	X-RAY DIFFRACTION	11	A	-6 - 31
12	X-RAY DIFFRACTION	12	A	40 - 209
13	X-RAY DIFFRACTION	13	A	212 - 279
14	X-RAY DIFFRACTION	14	A	280 - 393
15	X-RAY DIFFRACTION	15	A	413 - 510
16	X-RAY DIFFRACTION	16	B	-6 - 31
17	X-RAY DIFFRACTION	17	B	121 - 209
18	X-RAY DIFFRACTION	18	B	212 - 279
19	X-RAY DIFFRACTION	19	B	280 - 393
20	X-RAY DIFFRACTION	20	B	413 - 510

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