PDB-8jvt: Crystal structure of the chimeric protein mkaL2_v1

ID or keywords:

Entry

Database: PDB / ID: 8jvt

Title

Crystal structure of the chimeric protein mkaL2_v1

Components

mkaL2_v1

Keywords

RIBOSOMAL PROTEIN / OB fold

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.106 Å

Authors

Yagi, S. / Tagami, S.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	18H01328	Japan
Japan Society for the Promotion of Science (JSPS)	20K15854	Japan
Japan Society for the Promotion of Science (JSPS)	22H01346	Japan

Citation

Journal: Nat Commun / Year: 2024
Title: An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins.
Authors: Yagi, S. / Tagami, S.

History

Deposition	Jun 28, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jvt.cif.gz	134.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8jvt.ent.gz	108.9 KB	Display	PDB format
PDBx/mmJSON format	8jvt.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/jv/8jvt ftp://data.pdbj.org/pub/pdb/validation_reports/jv/8jvt	HTTPS FTP

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Related structure data

Related structure data	8jvnC 8jvoC 8jvpC 8jvqC 8jvrC 8jvsC 8jvuC 8jvvC 8jvwC 8jvxC 8jvyC 8jvzC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: mkaL2_v1

B: mkaL2_v1

C: mkaL2_v1

D: mkaL2_v1

E: mkaL2_v1

F: mkaL2_v1

36.1 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: mkaL2_v1

B: mkaL2_v1

defined by author&software
Evidence: gel filtration
12 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: mkaL2_v1

E: mkaL2_v1

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

3

D: mkaL2_v1

F: mkaL2_v1

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

Unit cell

Length a, b, c (Å)	124.137, 53.887, 55.654
Angle α, β, γ (deg.)	90.00, 113.41, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	mkaL2_v1 Mass: 6010.080 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 6000, 100mM Tris pH8.0, 200mM Lithium chrolide

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 35872 / % possible obs: 93.3 % / Redundancy: 1.82 % / CC_1/2: 0.99 / Net I/σ(I): 0.78
Reflection shell	Resolution: 2.1→2.2 Å / Num. unique obs: 5832 / CC_1/2: 0.44

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.106→38.684 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2484	3596	10.03 %
R_work	0.2021	-	-
obs	0.2069	35859	93.54 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.106→38.684 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2397	0	0	23	2420

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2424
X-RAY DIFFRACTION	f_angle_d	1.267	3273
X-RAY DIFFRACTION	f_dihedral_angle_d	30.54	960
X-RAY DIFFRACTION	f_chiral_restr	0.521	393
X-RAY DIFFRACTION	f_plane_restr	0.007	429

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 (%)
2.106-2.1336	0.3824	123	0.3421	1237	X-RAY DIFFRACTION	90
2.1336-2.1628	0.3784	158	0.3333	1250	X-RAY DIFFRACTION	95
2.1628-2.1937	0.3792	143	0.3413	1246	X-RAY DIFFRACTION	95
2.1937-2.2265	0.3577	127	0.3549	1253	X-RAY DIFFRACTION	95
2.2265-2.2613	0.3555	146	0.3272	1268	X-RAY DIFFRACTION	95
2.2613-2.2983	0.2986	142	0.3135	1236	X-RAY DIFFRACTION	95
2.2983-2.338	0.338	126	0.3176	1311	X-RAY DIFFRACTION	94
2.338-2.3805	0.3419	131	0.3248	1192	X-RAY DIFFRACTION	94
2.3805-2.4262	0.3909	131	0.3221	1266	X-RAY DIFFRACTION	91
2.4262-2.4758	0.3374	148	0.3149	1193	X-RAY DIFFRACTION	94
2.4758-2.5296	0.4009	133	0.2954	1303	X-RAY DIFFRACTION	97
2.5296-2.5884	0.3161	142	0.2957	1295	X-RAY DIFFRACTION	97
2.5884-2.6531	0.3645	145	0.2907	1255	X-RAY DIFFRACTION	97
2.6531-2.7248	0.3433	138	0.3099	1288	X-RAY DIFFRACTION	97
2.7248-2.805	0.3213	148	0.2723	1321	X-RAY DIFFRACTION	97
2.805-2.8955	0.3397	133	0.2922	1266	X-RAY DIFFRACTION	97
2.8955-2.999	0.3463	145	0.287	1278	X-RAY DIFFRACTION	96
2.999-3.119	0.314	147	0.263	1238	X-RAY DIFFRACTION	94
3.119-3.2609	0.3122	155	0.2325	1202	X-RAY DIFFRACTION	92
3.2609-3.4327	0.2831	120	0.2338	1204	X-RAY DIFFRACTION	91
3.4327-3.6476	0.2491	136	0.2135	1179	X-RAY DIFFRACTION	88
3.6476-3.929	0.2668	139	0.1869	1179	X-RAY DIFFRACTION	89
3.929-4.3239	0.1842	123	0.1512	1180	X-RAY DIFFRACTION	89
4.3239-4.9485	0.1723	132	0.1311	1182	X-RAY DIFFRACTION	89
4.9485-6.2304	0.2131	145	0.1517	1220	X-RAY DIFFRACTION	92
6.2304-38.684	0.185	140	0.1417	1221	X-RAY DIFFRACTION	92

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	2.4175	1.0646	-2.7716	6.3508	-1.8236	5.8825	0.0131	-0.2799	0.1367	-0.3775	-0.0328	1.0733	0.2546	-0.0038	0.1533	0.522	0.0411	-0.1074	0.4455	-0.0736	0.7183	23.3026	2.3073	22.904
2	2.4946	1.5381	0.8606	3.8644	3.9033	4.1781	-0.1086	1.6029	-1.2277	-0.4283	-0.006	0.0896	0.7464	-0.4959	0.1178	0.6431	0.0013	-0.0792	0.6744	-0.1901	0.7272	18.6428	-1.3655	18.4559
3	4.756	3.0283	-2.086	4.031	1.4856	9.3927	0.0185	-0.1049	-0.66	0.1711	-0.0179	-0.5254	0.3777	0.1537	0.0968	0.5035	0.061	-0.0761	0.3275	-0.0265	0.4798	21.9292	1.603	25.7672
4	6.8532	4.6475	1.0355	4.2174	3.525	8.2186	-0.3625	-0.7023	1.3694	0.0887	-0.1349	0.3793	-0.6245	-0.091	0.7981	0.578	0.0734	-0.0415	0.3543	-0.066	0.5718	14.2807	10.6502	27.6698
5	9.8577	2.2099	8.8395	2.5375	3.5942	9.2631	1.8909	1.2862	-1.9042	-1.1907	-0.688	1.4108	2.2079	0.6346	-0.4334	0.9299	0.0416	-0.3369	0.5826	-0.1905	0.8218	3.2782	-1.4153	20.5994
6	3.6179	3.4789	-0.3668	3.5443	-0.5073	3.1578	-0.0213	0.1487	0.5859	-0.7189	-0.2936	0.0042	-0.6003	0.1634	0.0481	0.4702	-0.0073	-0.0438	0.3863	-0.0258	0.6404	14.8794	11.0212	21.3249
7	6.2467	0.9112	-1.0304	4.9003	-0.2383	4.8827	0.3626	-0.9965	0.2728	0.1096	-0.0355	0.1278	0.1142	-0.3691	-0.3002	0.5704	-0.0258	-0.0532	0.3072	-0.0457	0.5269	12.5171	4.8512	30.806
8	4.1554	-1.4454	3.6563	8.3495	-4.4082	4.1252	-0.8958	-0.2589	0.0139	0.5582	0.826	0.2034	-0.2069	-0.9523	-0.0085	0.6114	0.2024	-0.016	1.0265	-0.1376	0.4847	12.4147	4.0827	-6.031
9	2.1955	0.1904	0.6181	2.0006	-7.2971	4.895	-2.8542	-2.4179	-0.1447	1.1578	1.6034	1.2951	-0.6619	-1.4534	0.2365	0.8862	0.1906	-0.0799	1.7607	0.165	1.1317	0.9061	5.3983	-4.7729
10	9.4661	-6.3529	-0.7899	9.2821	-2.4497	5.1884	-1.3034	-2.5796	0.967	1.1747	1.0855	-0.9979	-0.498	-0.2962	0.2104	0.5439	0.0525	-0.0289	0.982	-0.2296	0.5449	13.1396	8.2459	-6.1313
11	6.5414	-3.5527	0.4124	6.0316	-2.649	5.1756	0.3745	-0.043	-0.2455	0.3941	0.0381	0.06	0.5673	-0.0196	-0.4499	0.8037	0.0219	-0.0552	1.0061	-0.0672	0.506	18.7704	-13.8578	-2.2818
12	8.1446	1.3766	0.789	9.6617	-0.5686	2.437	-1.0488	-1.5365	-0.2386	0.8	0.5625	-0.1675	0.7186	-0.1536	0.3248	0.7948	0.0492	0.1246	0.8002	-0.0287	0.425	21.6189	-12.2874	-1.4143
13	8.8883	-1.7608	2.0732	2.0194	-0.5837	2.9447	-0.534	-1.1175	-1.1892	1.3308	0.3687	0.0845	1.4314	-0.77	0.4608	1.1545	-0.0678	0.1762	0.9089	0.1346	0.6766	21.1819	-24.6289	0.2339
14	2.0615	0.608	3.1643	5.9997	2.3621	8.734	-0.018	-0.1103	0.6389	-0.3707	0.0412	-0.181	-0.3481	-1.5433	-0.331	0.5038	0.0927	0.0036	0.7346	0.1285	0.5594	-11.007	11.1946	17.3114
15	4.6683	-6.9051	-0.3447	1.9787	0.7266	6.2766	-0.1343	1.6973	0.2036	-0.8286	0.2635	-0.7	0.7936	1.9693	-0.1845	0.6752	-0.0472	0.0936	1.1791	0.0479	0.8903	5.6801	10.9236	10.7879
16	7.3061	5.0203	-5.8172	3.5947	-4.0471	4.7775	0.1841	0.2759	0.2568	0.9044	0.3856	0.1704	0.081	-0.3002	-0.3125	0.4928	0.0291	-0.0204	0.7333	0.0359	0.5681	-9.3113	5.0558	17.3931
17	3.0837	-1.8083	-1.5626	6.5747	-1.2397	6.5576	-0.0862	0.9613	1.5595	0.0667	0.1554	0.3066	0.0612	-0.6633	-0.0935	0.5824	0.0003	-0.0581	0.5915	0.2752	0.5974	-8.7779	15.7329	12.8734
18	3.3493	4.1052	0.7867	5.9949	-2.2522	8.0028	-1.4161	-1.4312	-1.899	-0.2916	0.0587	-1.4359	1.6353	1.4936	1.2401	0.7939	0.2037	0.1312	0.6611	-0.0227	0.8687	43.0992	2.3209	9.794
19	7.8065	-2.1781	-8.3541	2.1554	1.7451	9.0927	1.6581	1.3591	2.0532	-0.5787	0.0364	-0.8908	-0.0177	-2.6469	-0.815	0.9224	-0.0068	-0.1812	0.9758	0.2112	0.99	25.4226	6.1539	7.3064
20	8.6399	1.4757	0.4231	2.3596	-1.5519	2.254	0.9315	0.365	-1.9147	-0.1467	-0.3623	-0.8379	0.2921	1.7293	-0.2432	0.5954	0.0828	0.0845	1.0351	-0.1484	0.7093	39.1269	5.2156	12.6907
21	4.9941	0.5764	-3.3296	9.5711	-4.3824	7.5386	-0.6317	-0.8709	-0.4416	-0.4073	0.1714	-1.4147	1.0445	1.1301	0.3448	0.6791	0.1419	0.0904	0.9104	-0.201	0.6439	39.5402	3.4586	10.317
22	7.3583	3.0821	-3.3092	3.9423	-0.2511	2.0528	-0.3879	1.3857	-1.1397	-1.4052	-0.1159	-0.7395	2.2589	1.6278	0.8492	1.0599	0.2785	0.2012	1.3373	-0.0865	0.7236	44.6262	3.9404	-0.1468

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 34 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 55 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 16 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 17 through 24 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 25 through 39 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 40 through 55 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 4 through 29 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 30 through 34 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 35 through 55 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 4 through 23 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 24 through 48 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 49 through 55 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 5 through 16 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 17 through 24 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 25 through 39 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 40 through 55 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 5 through 16 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 17 through 23 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 24 through 30 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 31 through 48 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 49 through 55 )

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