PDB-5x15: Crystal structure of Streptomyces coelicolor RraAS2, an unusual m...

ID or keywords:

Entry

Database: PDB / ID: 5x15

Title

Crystal structure of Streptomyces coelicolor RraAS2, an unusual member of the RNase ES inhibitor RraA protein family

Components

Putative transferase

Keywords

TRANSFERASE INHIBITOR / Rnase ES inhibitor / Streptomyces coelicolor / RraAS2 / RraA protein family / TRANSFERASE

Function / homology

4-hydroxy-4-methyl-2-oxoglutarate aldolase / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / transferase activity / Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase

Function and homology information

Biological species

Streptomyces coelicolor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.094 Å

Authors

Park, N. / Jo, I. / Ha, N.-C.

Citation

Journal: J. Microbiol. / Year: 2017
Title: Crystal structure of Streptomyces coelicolor RraAS2, an unusual member of the RNase E inhibitor RraA protein family
Authors: Park, N. / Heo, J. / Song, S. / Jo, I. / Lee, K. / Ha, N.C.

History

Deposition	Jan 24, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 17, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5x15.cif.gz	245 KB	Display	PDBx/mmCIF format
PDB format	pdb5x15.ent.gz	202.7 KB	Display	PDB format
PDBx/mmJSON format	5x15.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5x15_validation.pdf.gz	448 KB	Display	wwPDB validaton report
Full document	5x15_full_validation.pdf.gz	458.5 KB	Display
Data in XML	5x15_validation.xml.gz	23 KB	Display
Data in CIF	5x15_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x1/5x15 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/5x15	HTTPS FTP

-
Related structure data

Similar structure data	3shp-1 4wgf-d 1yf9-2 2x18-d 4wh0-d 3n2n-d 5cgz-1 6v23-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative transferase

B: Putative transferase

C: Putative transferase

88.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative transferase

B: Putative transferase

C: Putative transferase

A: Putative transferase

B: Putative transferase

C: Putative transferase

defined by author&software
177 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.914, 96.914, 166.556
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Putative transferase / RraA family protein Mass: 29551.135 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria) Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO7163 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FBS9

#1: Protein

Putative transferase / RraA family protein

Mass: 29551.135 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO7163 / Plasmid: pET-15b / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FBS9

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.16 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M NaCl, 0.1M bis-Tris propane, PEG 1500

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2823 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2823 Å / Relative weight: 1
Reflection	Resolution: 3.09→50 Å / Num. obs: 13795 / % possible obs: 98.3 % / Redundancy: 8.6 % / R_merge(I) obs: 0.084 / Net I/σ(I): 36.4
Reflection shell	Resolution: 3.1→3.15 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.351 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 826 / % possible all: 98.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-2000		data processing
HKL-2000		data scaling
DENZO		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 3.094→48.457 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.55 / Phase error: 32.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3008	650	4.71 %
R_work	0.2444	-	-
obs	0.2473	13795	80.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.094→48.457 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4555	0	0	0	4555

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4654
X-RAY DIFFRACTION	f_angle_d	0.62	6334
X-RAY DIFFRACTION	f_dihedral_angle_d	6.64	2767
X-RAY DIFFRACTION	f_chiral_restr	0.045	709
X-RAY DIFFRACTION	f_plane_restr	0.005	831

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 (%)
3.094-3.3328	0.2879	56	0.2442	1066	X-RAY DIFFRACTION	33
3.3328-3.6681	0.3415	89	0.2482	2312	X-RAY DIFFRACTION	72
3.6681-4.1987	0.3283	129	0.2358	3197	X-RAY DIFFRACTION	97
4.1987-5.2888	0.265	165	0.2175	3215	X-RAY DIFFRACTION	99
5.2888-48.4629	0.3068	211	0.2686	3355	X-RAY DIFFRACTION	100

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	7.2755	1.5314	1.0743	5.2021	0.05	1.9068	0.0173	-0.2402	0.3178	0.6247	-0.0403	-0.9039	-0.3484	1.0047	0.1797	0.3231	-0.0365	-0.3739	0.9408	-0.0055	0.6934	43.0992	63.8343	110.8873
2	2.2003	-1.6537	-0.1694	2.7254	-1.2531	1.9914	0.0707	-0.1074	0.0707	0.0426	0.0281	0.0817	-0.1901	-0.2444	0.26	0.6851	-0.0202	-0.1889	0.4341	-0.3944	0.0882	26.7637	59.54	104.8049
3	0.653	0.1791	0.4566	1.1444	0.1639	0.9588	-0.0074	-0.3424	-0.1062	0.49	-0.1893	-0.4091	-0.0985	0.0609	-0.2557	-0.1085	0.0105	-0.3401	0.3744	-0.0447	-0.1612	40.044	53.4807	96.1288
4	6.3268	-1.8915	5.3539	2.1988	-2.2981	6.286	0.589	0.6156	-0.4829	0.7145	-0.3403	-0.8953	0.1521	1.261	-0.1941	0.4481	-0.1375	-0.127	0.5002	0.2796	0.5787	50.4157	58.3073	81.5379
5	1.7681	-0.6561	-1.1328	0.73	0.028	1.041	-0.5312	-0.3983	0.6568	0.4184	0.0266	-0.5481	-0.6148	0.5211	0.3971	0.3499	-0.2105	-0.3768	0.4788	0.1622	0.2653	46.4572	59.4646	96.7367
6	2.8737	-1.2143	0.3909	0.999	-0.1639	0.366	-0.0708	-0.1742	-0.1029	0.1064	-0.2196	-0.3694	0.1393	0.4811	-0.2844	-0.083	0.2044	-0.0327	0.452	0.2249	0.3042	45.8712	48.6587	86.9467
7	3.7703	0.0919	2.3291	1.5753	1.2596	3.6014	-0.1369	0.0805	0.3443	0.1665	0.039	-0.4793	-0.1585	0.6208	0.2666	0.1792	-0.0774	-0.3122	0.6262	0.4458	0.5005	51.1683	53.6119	97.1867
8	1.0995	-0.6353	-0.2566	0.3871	0.1462	0.2259	0.0909	-0.0807	-0.15	0.3189	-0.0138	-0.7913	0.4416	0.5719	0.3325	0.539	0.4531	-0.32	0.521	0.1398	0.5034	48.7401	43.3131	94.7697
9	4.2916	-1.5507	1.522	1.4671	-0.1027	3.1647	0.0971	0.6892	0.2565	-0.0518	-0.0725	-0.2245	-0.0646	0.422	0.2673	0.1148	0.125	-0.0807	0.4418	0.1895	0.2098	43.8215	45.1929	87.8863
10	0.026	-0.1252	-0.0051	0.3533	-0.1118	0.4699	-0.1918	0.1791	0.3959	0.2042	-0.0038	-0.2097	-0.3279	0.0973	-0.0032	0.1545	0.0195	-0.5523	0.1677	0.4832	0.1797	40.5926	59.5223	89.1011
11	3.4957	-1.6436	0.7452	2.9643	-0.8661	2.3831	-0.3822	0.0491	-0.0633	0.4645	0.106	0.1351	-0.1678	0.1376	0.0967	0.2074	0.1499	-0.0689	0.4307	0.0979	0.7123	34.1799	58.5422	103.6239
12	1.8247	1.8454	-2.4171	3.2252	-1.2092	4.256	0.266	-0.6374	-0.3837	0.0062	0.3666	0.1781	-0.2122	-0.0853	-0.3996	0.2025	0.1159	-0.1034	0.8255	-0.0507	0.8284	28.2533	56.8235	119.2049
13	1.5415	1.1855	1.0656	0.9111	0.8183	0.7349	0.1956	0.2024	-0.1197	0.0887	0.3093	0.3095	0.2464	0.1026	0.0007	1.2542	0.9631	-0.3287	1.4755	-0.0975	1.3332	57.6377	21.6855	79.2079
14	2.8126	-1.8999	0.0728	4.3374	-0.5212	1.2367	-0.0951	-0.3353	0.5982	0.089	-0.0524	-0.4951	0.2401	0.4977	0.2674	0.3335	0.448	0.06	0.9583	0.0861	0.5176	54.2606	37.2194	80.2972
15	0.7762	-0.1987	-0.2495	0.0932	0.2658	0.7714	0.2439	0.0701	-0.3512	-0.1975	0.0034	-0.0692	0.4198	0.4526	0.3712	0.5041	0.8194	0.0051	0.4888	-0.0796	0.5171	42.6063	30.0345	81.7366
16	4.1545	-0.3091	1.5453	0.8964	-1.057	1.5793	0.2686	-0.0338	-1.1884	-0.5349	0.1317	-0.3469	0.7947	0.2356	-0.1881	0.5658	0.2751	-0.2836	0.2324	-0.2227	0.6188	34.6675	16.5077	79.5681
17	5.799	-4.3546	2.5666	4.1959	-2.0324	1.1467	-0.0345	-0.543	-0.8482	0.6184	-0.1919	-0.082	0.0736	0.155	0.0633	1.1094	0.3635	-0.0771	0.362	0.2236	0.635	34.0718	18.9035	88.3417
18	2.9487	-2.2003	0.6336	3.1059	0.7224	1.1193	-0.5197	-0.3853	-0.5193	0.784	0.2417	0.1905	0.8382	0.3147	0.3741	1.0349	0.3075	0.3145	0.2675	-0.0204	0.311	37.001	22.6861	88.3017
19	1.7337	-0.6328	0.4399	0.2469	-0.3512	1.7398	0.1579	-0.8372	-0.4461	0.2581	0.2006	0.1144	0.3411	-0.1066	0.4304	0.9512	0.2873	-0.1149	0.3417	0.2384	-0.0721	35.7131	24.19	94.4594
20	3.8413	0.4737	-3.3799	0.1245	-0.6346	3.685	-0.8079	0.1547	-1.1727	0.1607	-1.0227	0.3374	1.718	-0.2115	1.5915	1.3392	-0.1312	0.0706	0.4781	-0.1	1.1995	24.7578	20.2688	80.8299
21	3.1088	-0.9602	-0.0614	1.0193	0.5241	1.5496	0.3963	0.3137	-1.0332	-0.4822	-0.1702	-0.3638	0.716	0.3542	-0.2066	0.6209	0.6982	-0.0419	0.4094	0.1611	0.4567	45.2983	28.2694	76.713
22	0.2912	-0.2828	0.398	2.1386	1.4333	2.5833	-0.0038	-0.3838	0.0522	-0.0937	-0.471	-0.5264	0.0814	0.6927	-0.3282	0.3843	0.2211	0.1584	1.8265	0.2797	0.9039	64.3944	42.367	85.5841
23	9.3791	-5.7085	4.7887	9.0997	-4.1776	4.5968	-0.6889	-2.3819	-1.174	1.9786	0.8019	0.7116	0.2434	-0.573	0.0297	1.2905	-0.1269	0.3034	0.9616	0.0789	0.8172	14.6794	20.7754	110.803
24	0.6107	-0.4337	0.3303	1.3742	0.488	2.7413	0.0288	-0.086	-0.1155	0.1468	-0.149	-0.3121	1.3437	-0.0205	0.2977	0.5251	-0.2122	0.3226	0.4964	0.1848	0.0189	18.7912	28.3828	99.0911
25	1.2721	-0.9828	1.7463	3.414	-1.621	2.9582	-0.1057	-0.3851	-0.0913	0.8174	0.3412	0.0644	-0.5784	-0.628	-0.0289	0.8602	-0.0738	-0.0808	1.2169	0.0072	0.1557	10.658	47.9875	108.9718
26	2.1284	0.867	-1.3279	2.8183	-0.9129	4.4165	-0.0766	-0.8636	-0.445	0.9206	0.0856	0.2633	0.4249	-0.1825	-0.08	0.8716	-0.0533	0.0267	0.8117	0.1764	0.0199	15.1859	33.6598	109.877
27	0.7655	-0.1664	0.4323	3.17	-2.4992	4.3276	0.1061	-0.9817	0.096	0.4524	-0.4982	0.1454	0.1904	-0.0622	0.2342	0.3135	-0.1615	0.0406	0.5301	0.0823	0.1788	21.7965	41.8622	108.6208
28	1.1921	-0.0243	-0.2438	7.27	-2.2831	0.77	-0.1471	-0.8343	-0.1212	0.3686	-0.3454	-0.6367	-0.1035	0.2177	0.3739	0.4242	0.2628	-0.0072	0.6379	0.1136	0.1455	28.3287	41.8641	107.2715
29	0.9533	0.4945	0.6187	3.335	2.548	2.0075	0.1564	-0.111	0.1858	0.7565	-0.2723	0.6427	0.3989	-0.8385	0.2638	0.235	0.0664	0.157	0.9347	0.0012	0.1651	11.416	40.457	101.6895
30	1.0721	-0.8246	-1.1546	6.1301	-1.0447	3.4073	0.0126	-0.0427	-0.6298	0.0932	0.1154	0.2615	0.277	-0.2871	0.0661	1.0319	-0.4832	-0.1927	0.5101	0.1357	0.5977	20.6253	25.0798	101.3659
31	6.3721	-2.3695	-1.7036	0.8693	0.5736	3.7682	-0.3617	0.1746	0.1677	1.0255	-0.1025	0.9068	1.4636	0.1533	0.6086	1.3957	-0.2962	0.1599	0.6158	0.0596	1.2068	22.9426	9.0245	100.2228

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 34 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 88 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 114 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 115 through 124 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 125 through 139 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 140 through 153 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 154 through 169 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 170 through 179 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 180 through 208 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 209 through 220 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 221 through 242 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 33 through 43 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 44 through 57 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 58 through 87 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 88 through 124 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 125 through 144 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 145 through 158 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 159 through 177 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 178 through 188 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 189 through 221 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 222 through 244 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 31 through 47 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 48 through 88 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 89 through 114 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 115 through 124 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 125 through 158 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 159 through 178 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 179 through 204 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 205 through 217 )
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 218 through 241 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi