PDB-4chg: Crystal structure of VapBC15 complex from Mycobacterium tuberculosis

ID or keywords:

Entry

Database: PDB / ID: 4chg

Title

Crystal structure of VapBC15 complex from Mycobacterium tuberculosis

Components

ANTITOXIN VAPB15
PROBABLE RIBONUCLEASE VAPC15

Keywords

TOXIN/ANTITOXIN / TOXIN-ANTITOXIN COMPLEX / PIN DOMAIN

Function / homology

Function and homology information

positive regulation of growth / negative regulation of growth / RNA nuclease activity / Hydrolases; Acting on ester bonds / response to hypoxia / magnesium ion binding / metal ion binding
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Das, U. / Pogenberg, V. / Tiruttani Subhramanyam, U.K. / Wilmanns, M. / Srinivasan, A. / Gourinath, S.

Citation

Journal: J.Struct.Biol. / Year: 2014
Title: Crystal Structure of the Vapbc-15 Complex from Mycobacterium Tuberculosis Reveals a Two-Metal Ion Dependent Pin-Domain Ribonuclease And a Variable Mode of Toxin-Antitoxin Assembly.
Authors: Das, U. / Pogenberg, V. / Subhramanyam, U.K.T. / Wilmanns, M. / Gourinath, S. / Srinivasan, A.

History

Deposition	Dec 2, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2014	Group: Data collection / Database references
Revision 1.2	Mar 7, 2018	Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4chg.cif.gz	385.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4chg.ent.gz	320 KB	Display	PDB format
PDBx/mmJSON format	4chg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4chg_validation.pdf.gz	491.2 KB	Display	wwPDB validaton report
Full document	4chg_full_validation.pdf.gz	496.9 KB	Display
Data in XML	4chg_validation.xml.gz	44.4 KB	Display
Data in CIF	4chg_validation.cif.gz	60.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ch/4chg ftp://data.pdbj.org/pub/pdb/validation_reports/ch/4chg	HTTPS FTP

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Related structure data

Similar structure data	5tcy-3 5tcy-2 3n21-d 5tcy-1 5t9q-d 5ix8-1 5l8p-d 3vo9-1 5wr6-d 2qob-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#3 - Mar 2000 DNA Polymerase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: PROBABLE RIBONUCLEASE VAPC15

B: PROBABLE RIBONUCLEASE VAPC15

C: PROBABLE RIBONUCLEASE VAPC15

D: PROBABLE RIBONUCLEASE VAPC15

E: PROBABLE RIBONUCLEASE VAPC15

F: PROBABLE RIBONUCLEASE VAPC15

G: ANTITOXIN VAPB15

H: ANTITOXIN VAPB15

I: ANTITOXIN VAPB15

J: ANTITOXIN VAPB15

hetero molecules

130 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PROBABLE RIBONUCLEASE VAPC15

B: PROBABLE RIBONUCLEASE VAPC15

G: ANTITOXIN VAPB15

H: ANTITOXIN VAPB15

hetero molecules

defined by author&software
50.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PROBABLE RIBONUCLEASE VAPC15

D: PROBABLE RIBONUCLEASE VAPC15

I: ANTITOXIN VAPB15

hetero molecules

defined by author&software
40.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: PROBABLE RIBONUCLEASE VAPC15

F: PROBABLE RIBONUCLEASE VAPC15

J: ANTITOXIN VAPB15

hetero molecules

defined by author&software
40.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.160, 131.200, 149.350
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PROBABLE RIBONUCLEASE VAPC15 Mass: 15010.687 Da / Num. of mol.: 6 / Fragment: VAPC15-TOXIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P64925, UniProt: P9WF97*PLUS
#2: Protein	ANTITOXIN VAPB15 / RNASE VAPC15 / TOXIN VAPC15 / VAPBC15 Mass: 9964.924 Da / Num. of mol.: 4 / Fragment: VAPB15-ANTITOXIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q10848, UniProt: P9WLM7*PLUS, Hydrolases; Acting on ester bonds
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.3 Å³/Da / Density % sol: 62.7 % / Description: NONE
Crystal grow	pH: 7 Details: 100 MM SODIUM HEPES PH. 7.0, 8% PEG 8000 AND 10 MM BME

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.977316
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2013 / Details: SLITS AND COLLIMATOR
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977316 Å / Relative weight: 1
Reflection	Resolution: 2.1→60.06 Å / Num. obs: 189170 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / B_iso Wilson estimate: 25.31 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 14.1
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 13.1 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 4.5 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
iMOSFLM		data reduction
SCALEPACK		data scaling
Auto-Rickshaw		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.1→60.062 Å / SU ML: 0.21 / σ(F): 1.13 / Phase error: 18.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1997	9467	5 %
R_work	0.1674	-	-
obs	0.1691	189140	99.09 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→60.062 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7174	0	8	551	7733

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7277
X-RAY DIFFRACTION	f_angle_d	0.97	9860
X-RAY DIFFRACTION	f_dihedral_angle_d	12.166	2700
X-RAY DIFFRACTION	f_chiral_restr	0.063	1163
X-RAY DIFFRACTION	f_plane_restr	0.003	1287

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 (%)
2.1-2.1239	0.3176	309	0.2605	6018	X-RAY DIFFRACTION	100
2.1239-2.1489	0.31	299	0.2477	6059	X-RAY DIFFRACTION	100
2.1489-2.1751	0.2679	363	0.2348	5971	X-RAY DIFFRACTION	100
2.1751-2.2026	0.2641	297	0.2219	6028	X-RAY DIFFRACTION	100
2.2026-2.2316	0.2163	309	0.2123	6061	X-RAY DIFFRACTION	100
2.2316-2.2621	0.2268	326	0.1979	6073	X-RAY DIFFRACTION	100
2.2621-2.2945	0.2185	304	0.1901	5940	X-RAY DIFFRACTION	100
2.2945-2.3287	0.2417	370	0.1896	6085	X-RAY DIFFRACTION	100
2.3287-2.3651	0.2174	355	0.1844	5923	X-RAY DIFFRACTION	100
2.3651-2.4039	0.2058	300	0.1781	5918	X-RAY DIFFRACTION	98
2.4039-2.4453	0.1878	288	0.1682	5784	X-RAY DIFFRACTION	95
2.4453-2.4898	0.1959	315	0.161	6040	X-RAY DIFFRACTION	99
2.4898-2.5377	0.2034	291	0.1651	6036	X-RAY DIFFRACTION	100
2.5377-2.5895	0.2211	284	0.1648	6027	X-RAY DIFFRACTION	100
2.5895-2.6458	0.2134	333	0.1585	5985	X-RAY DIFFRACTION	100
2.6458-2.7073	0.1948	294	0.1533	6111	X-RAY DIFFRACTION	100
2.7073-2.775	0.2182	281	0.1603	6092	X-RAY DIFFRACTION	100
2.775-2.8501	0.2037	311	0.1666	5992	X-RAY DIFFRACTION	99
2.8501-2.9339	0.198	319	0.166	6019	X-RAY DIFFRACTION	100
2.9339-3.0286	0.2207	329	0.1768	6004	X-RAY DIFFRACTION	100
3.0286-3.1369	0.1999	314	0.1754	5845	X-RAY DIFFRACTION	96
3.1369-3.2625	0.2033	292	0.1847	5889	X-RAY DIFFRACTION	98
3.2625-3.4109	0.2022	322	0.1685	6056	X-RAY DIFFRACTION	100
3.4109-3.5907	0.2066	329	0.1606	6002	X-RAY DIFFRACTION	100
3.5907-3.8157	0.2082	321	0.153	6020	X-RAY DIFFRACTION	100
3.8157-4.1102	0.1567	299	0.1367	6060	X-RAY DIFFRACTION	100
4.1102-4.5237	0.1672	333	0.1319	5981	X-RAY DIFFRACTION	99
4.5237-5.178	0.1571	330	0.1382	5768	X-RAY DIFFRACTION	96
5.178-6.5225	0.1859	360	0.1667	5999	X-RAY DIFFRACTION	100
6.5225-60.0861	0.1602	290	0.1635	5887	X-RAY DIFFRACTION	97

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	3.7935	-1.7677	0.3148	2.5511	0.9204	3.1496	0.2067	0.1789	0.2869	-0.1545	-0.3399	-0.6137	-0.0257	0.276	0.0952	0.2045	0.0138	0.0556	0.3015	0.0433	0.3206	51.9683	0.9239	119.8702
2	2.386	1.4598	2.3456	2.375	-0.2851	4.2792	0.1648	-0.0601	0.3118	-0.1134	-0.2361	-0.3987	-0.2942	0.4597	0.0111	0.2127	0.0068	0.0792	0.3891	0.0883	0.4114	58.0453	4.8982	119.6798
3	2.3685	-0.8523	0.2543	0.316	-0.1184	0.0835	-0.123	-0.2136	0.5423	-0.056	0.1747	-0.4908	-0.4094	0.1805	-0.1217	0.257	-0.0719	0.0547	0.2666	0.0116	0.401	51.1246	10.8224	125.6815
4	1.1209	-0.0736	0.402	0.9485	-0.636	1.5232	0.1813	-0.067	0.0602	-0.1609	-0.0452	0.057	0.1376	-0.1054	-0.1203	0.268	-0.0166	0.0043	0.2574	-0.0212	0.2137	45.4578	-2.1373	131.0007
5	3.9518	-2.5893	2.0423	1.6807	-1.3614	1.2608	-0.1647	-0.3388	0.7202	0.1728	0.0193	-0.5359	-0.2589	0.1189	-0.1059	0.2102	-0.0244	0.0411	0.3672	-0.2286	0.2374	38.7055	10.6158	127.6145
6	1.4964	0.5934	0.771	1.8478	0.0082	3.4097	0.085	0.0148	-0.0331	-0.0762	-0.0766	0.0396	0.3721	0.0854	0.0053	0.2264	0.0171	-0.0055	0.1764	0.0079	0.2174	31.2114	6.3885	110.1608
7	2.0073	-0.0628	-0.1941	1.7989	0.5442	1.8777	0.0275	-0.0706	0.3921	0.4244	-0.0843	-0.1921	0.2347	0.2132	0.0628	0.2278	0.0176	0.0101	0.2336	0.044	0.2895	40.6428	8.6028	116.8541
8	4.1253	-1.6463	0.8408	2.623	-2.6327	4.708	0.0688	0.2798	0.1281	-0.2468	-0.1351	-0.2433	-0.1582	0.0293	-0.0082	0.2888	0.0351	0.0658	0.2279	0.0351	0.1802	40.6012	7.1088	107.1447
9	6.2405	-4.2456	0.6105	7.1298	-1.0775	1.7814	0.2007	0.4822	0.5307	-0.3228	-0.4225	-0.4852	0.159	0.4067	0.1018	0.2738	0.008	0.0729	0.301	0.1097	0.2798	48.6037	8.8032	110.6502
10	5.2139	0.0798	4.4261	2.8033	1.689	4.6753	0.0916	-0.2993	-0.0043	0.0634	-0.0213	0.8237	0.3983	-0.6144	-0.1056	0.327	-0.1153	-0.0625	0.263	0.0839	0.4102	16.7891	-3.7606	121.2039
11	1.542	-0.1869	-1.351	2.0427	-0.7881	1.6401	0.3056	0.1095	-0.4738	-0.4536	0.0934	0.7214	0.383	-0.8405	-0.3317	0.3839	-0.1658	-0.1546	0.4454	0.1065	0.5518	9.4452	-7.1181	118.2773
12	3.0499	1.0036	0.9455	0.3581	0.2857	0.312	0.2981	-0.0825	0.0559	0.1541	-0.032	0.518	0.0468	-0.4738	-0.165	0.2533	-0.057	0.0356	0.3586	0.1242	0.4012	12.8311	1.9018	127.6068
13	4.7821	-1.6485	-1.0514	4.7037	1.4535	7.6834	0.1461	0.013	0.5791	-0.3381	0.041	-0.3152	-0.8613	-0.0091	-0.1587	0.3408	-0.0257	-0.0603	0.2739	0.0407	0.3579	25.7808	3.6044	120.6416
14	2.1015	-0.573	-0.3502	1.4295	0.0359	1.1093	0.0877	0.1321	0.0095	-0.1971	-0.011	0.1301	0.0647	-0.175	-0.0535	0.2286	-0.0124	-0.0397	0.2164	0.0185	0.2395	18.1694	7.4175	113.3443
15	6.765	0.3675	4.1234	0.0106	0.1844	2.5253	-0.293	-0.4746	0.4877	0.178	0.0284	0.1065	-0.014	-0.5422	0.0941	0.2722	-0.0097	0.0345	0.3008	-0.1125	0.4139	24.4728	6.4663	129.5376
16	3.1083	-1.1841	-0.0313	3.2061	-1.7691	1.2264	0.0483	-0.2934	0.0731	0.4444	-0.0053	-0.1254	0.1906	-0.1789	-0.1105	0.2926	-0.031	-0.0415	0.255	0.0057	0.1909	36.5909	-7.1024	132.3804
17	1.3785	-0.645	0.2259	3.7827	-1.7725	3.4168	0.0797	0.0554	-0.1805	-0.3787	-0.1162	0.2106	0.0113	-0.3808	0.0581	0.4296	-0.0014	-0.1102	0.2483	-0.0431	0.2649	33.5039	-14.141	124.3318
18	1.9891	0.1579	-0.398	0.6776	0.4292	2.2677	0.11	-0.0262	0.0043	-0.2202	0.063	0.3364	0.0005	-0.3194	-0.1758	0.2841	-0.045	-0.0622	0.2558	0.0498	0.2752	24.9846	-4.6159	129.0564
19	4.5916	0.3685	2.9384	4.0074	-1.7085	4.2476	0.2736	-0.1942	-0.1933	-0.3155	0.0335	0.1075	0.3587	-0.4668	-0.2142	0.3775	-0.0608	-0.0673	0.215	0.0714	0.2443	27.0716	-14.218	129.4387
20	3.4601	0.311	1.6796	1.4436	0.2393	4.0777	0.3279	-0.5091	-0.4096	-0.0122	0.1101	0.446	0.353	-0.6452	-0.1896	0.3198	-0.1256	-0.0816	0.3102	0.1427	0.3806	18.3852	-12.2601	128.8379
21	4.6716	-0.4665	-2.2262	2.0885	-0.488	3.0916	-0.0804	0.4959	-0.2633	-0.2404	0.0986	0.1706	0.3937	-0.6613	0.0219	0.2948	-0.0915	0.036	0.2771	0.053	0.2756	-10.5638	-9.829	86.621
22	0.9469	-0.0703	0.9177	1.578	0.6571	2.1573	0.0087	0.0573	-0.4317	-0.0632	0.1684	0.6293	0.6451	-0.7689	0.0004	0.4218	-0.2662	0.064	0.51	0.0977	0.4494	-17.8488	-13.7118	89.017
23	4.9981	2.3002	0.0185	1.3948	0.6311	1.2964	0.1234	0.0739	-0.8342	0.3187	-0.1666	-0.25	0.4839	-0.0072	0.0821	0.4134	-0.0749	-0.0345	0.2927	0.0309	0.458	-7.3329	-17.3246	81.9747
24	3.3885	2.0305	-1.9161	1.6767	0.4704	6.8802	0.0387	-0.2388	0.3722	0.1589	-0.1003	-0.6921	0.077	1.0449	0.0912	0.4487	-0.0466	-0.0438	0.4115	0.0958	0.4549	0.3447	-5.937	88.1963
25	3.6127	0.134	1.387	2.3044	1.5733	1.8169	0.1009	-0.3928	-0.1422	0.6501	0.0455	0.5303	-0.0115	-0.0114	-0.1631	0.3324	-0.109	0.0459	0.3795	0.0811	0.2251	-2.7349	-5.5508	98.902
26	3.3221	0.6569	0.8615	4.4136	1.441	3.492	-0.1014	-0.0888	-0.4444	0.2437	0.0361	0.1164	0.6187	0.1264	0.0463	0.4355	-0.0699	0.0327	0.3134	0.1231	0.4232	-1.5714	-14.927	96.3387
27	2.9617	2.9352	-2.994	2.8326	-2.9203	2.9849	-0.2805	0.2224	-0.5188	0.0925	0.176	0.0115	0.4066	0.0119	0.0953	0.4316	-0.0514	0.0186	0.2616	-0.0506	0.7027	3.4308	-10.5096	80.447
28	2.5033	-0.0587	1.6055	3.6725	-1.3896	3.2331	0.0691	0.128	-0.104	-0.161	0.0825	0.0696	-0.2322	-0.1717	-0.1225	0.1957	-0.0214	0.0163	0.1846	0.0034	0.1733	-2.8974	6.7368	74.6193
29	3.0479	1.0258	-0.6516	2.3675	0.1097	1.6079	-0.2206	0.0238	-0.3502	0.2299	0.1102	-0.0909	0.3243	-0.0847	0.0879	0.2876	-0.0468	0.0067	0.257	0.0378	0.2572	-5.5634	-4.1991	78.1454
30	2.4449	-0.6545	-0.1143	4.314	-2.0861	6.3673	0.1523	0.2354	0.2457	-0.1274	0.2323	0.1312	-0.0728	-0.6814	-0.3056	0.2168	-0.0116	0.0191	0.39	0.0647	0.2888	-12.3895	2.2329	75.1468
31	3.0147	0.5385	-1.8887	2.0413	-0.3107	4.6633	-0.1501	0.2467	-0.1591	-0.3658	0.1974	0.5308	0.3323	-0.6702	0.0065	0.2568	-0.0938	-0.0638	0.4201	0.0254	0.3455	-15.4743	-5.5382	77.1041
32	2.7081	1.1536	-1.3712	7.1456	-1.3436	4.1446	0.0717	-0.0093	-0.1729	0.2509	-0.0607	-0.4649	-0.1783	0.4847	-0.0358	0.238	-0.0691	0.0028	0.2909	-0.0545	0.2152	13.921	14.0393	85.0059
33	3.397	1.4644	-0.2007	0.9095	-0.1136	5.0533	0.0158	0.2051	0.0359	0.0773	0.0374	-0.0632	-0.8328	0.1528	-0.0667	0.3602	-0.1082	0.0125	0.2943	-0.0188	0.2188	17.6259	21.8444	84.865
34	1.9959	-0.5347	0.464	0.9267	-0.4546	1.9169	0.0449	-0.0009	-0.1441	-0.1381	0.1094	-0.0226	0.0539	0.027	-0.147	0.2829	-0.0527	0.0346	0.2583	-0.0494	0.2375	11.0388	10.5172	75.8267
35	1.694	4.074	-1.9203	9.6773	-4.6017	2.1626	-0.0297	0.0032	-0.3947	-0.1658	-0.1769	-0.2341	0.1597	0.153	0.1027	0.403	0.0047	0.1055	0.2706	-0.1047	0.3517	14.3478	-0.79	81.5883
36	2.9571	0.5993	0.0395	2.185	0.2937	4.3972	0.3644	-0.2782	-0.2162	-0.0226	-0.0135	-0.0092	-0.2348	-0.2678	-0.3255	0.2548	-0.0259	0.0171	0.1951	0.0508	0.2141	4.4912	0.0265	98.2751
37	2.2986	-0.2894	0.4904	1.7916	-0.3889	1.5544	0.1806	0.0379	-0.195	-0.0793	-0.0369	-0.1587	0.0006	0.0995	-0.126	0.2416	-0.0443	-0.0046	0.2187	-0.0049	0.2273	11.7568	5.8359	94.38
38	3.2368	-0.6999	0.4049	7.6655	-2.4858	4.1359	0.3373	-0.1277	0.0927	0.1729	-0.2976	-0.6385	-0.5104	0.7023	-0.181	0.2705	-0.0841	-0.0024	0.2577	-0.0184	0.2263	16.9163	11.9779	96.1006
39	3.1076	-2.3478	2.0719	4.7022	0.5561	2.9513	0.229	-0.3544	0.0651	0.3056	-0.0654	0.6606	0.2271	-0.2729	-0.1672	0.2559	0.0205	0.1141	0.3975	-0.0247	0.3381	4.826	36.0446	120.1833
40	1.0943	-0.0598	0.012	1.5095	-0.4093	0.1181	-0.0833	-0.3564	0.4447	0.4603	0.0907	0.9851	-0.2291	-0.6039	-0.2761	-0.0844	0.2494	0.3555	0.7508	-0.1862	0.4711	-3.0085	37.2723	122.7781
41	1.5132	-0.1028	0.6507	2.9037	-1.2815	2.4512	-0.2436	-0.1695	0.2361	0.4778	0.0858	-0.1693	-0.0876	-0.2808	0.0266	0.3617	0.044	0.0724	0.3769	-0.0703	0.2688	11.5419	40.2851	120.5369
42	2.3998	-0.391	0.771	2.6251	-1.2714	3.52	-0.2311	-0.3398	0.4036	0.4646	-0.025	-0.11	0.047	-0.2048	0.171	0.368	0.1321	0.0574	0.3565	-0.0942	0.2805	11.4238	48.1272	124.6142
43	7.7994	-4.6774	-5.0458	3.7934	3.0107	3.2393	-0.167	-0.4247	-0.214	0.3173	-0.0859	0.0759	-0.1856	-0.1274	0.0791	0.3669	0.0286	0.0216	0.7395	-0.0806	0.1999	19.1686	33.1557	123.858
44	1.3114	0.5032	-0.127	2.7197	1.0323	1.8987	0.0153	-0.2664	-0.0991	-0.1529	-0.0437	-0.0019	0.0163	-0.0581	0.0369	0.1673	0.0041	0.0044	0.1989	0.0126	0.1365	17.3454	23.1703	107.1825
45	2.8329	-0.1019	-0.9341	1.2688	0.2439	1.7077	-0.0253	-0.4235	0.1185	0.2373	0.0843	0.1052	-0.2708	-0.0173	-0.0918	0.2543	0.0277	0.0408	0.2749	-0.0192	0.2	12.1228	27.946	116.9949
46	5.2108	0.4824	-1.2639	5.8588	2.8138	2.2198	0.0814	0.1514	0.0403	-0.0238	-0.0321	0.4165	-0.0426	-0.4217	-0.1188	0.2005	-0.0171	0.0181	0.2692	0.019	0.1804	7.512	22.7479	110.0987
47	5.4798	-2.6493	-0.287	4.924	0.2583	2.1043	-0.1473	0.115	-0.2485	0.3669	0.0307	0.6966	0.2913	-0.5517	0.0794	0.2083	-0.048	0.0437	0.3304	0.0397	0.3283	2.5033	25.189	117.0705
48	2.5374	-2.583	-0.9426	3.6421	-0.0865	6.502	-0.1331	0.0261	0.175	-0.214	0.0115	-0.4183	-0.821	0.6066	0.054	0.2051	-0.0606	0.037	0.2163	0.057	0.2543	32.9428	35.6462	100.6966
49	3.9185	-0.5011	-0.0982	3.9621	-0.5839	1.4376	0.155	0.5719	0.1734	-0.7303	-0.3619	-0.4165	-0.1217	0.5997	0.1004	0.2991	0.0233	0.128	0.2552	0.0343	0.2851	37.4859	34.7827	93.5855
50	3.2266	-1.1706	-2.7019	0.4397	1.0171	2.4324	-0.3994	-0.0262	0.1106	0.0582	-0.0092	-0.6632	-0.092	0.5423	0.2606	0.1964	-0.0364	0.0298	0.2951	0.058	0.47	40.1281	34.8677	106.7759
51	4.6798	0.9107	0.588	4.5368	2.2365	5.6259	0.1712	-0.8884	-0.3243	0.9471	0.0474	0.1312	0.5458	-0.5066	-0.1473	0.3401	0.0132	0.0256	0.3251	0.011	0.2644	25.8382	31.4448	109.0502
52	1.3024	-0.6755	-0.2192	0.8456	-0.3555	0.8647	0.0637	-0.058	0.0251	-0.1342	-0.076	-0.1168	0.1815	-0.0039	-0.001	0.195	0.0173	0.0318	0.1997	0.0023	0.1883	30.0902	22.4432	103.8209
53	4.6544	-4.0971	-5.7419	3.5929	5.057	7.0851	-0.0024	-0.3762	0.4034	0.3587	0.2894	-0.5035	-0.0009	0.2809	-0.1954	0.3078	0.1005	-0.0179	0.4046	-0.004	0.274	31.3809	34.8768	115.867
54	2.4575	-1.1033	0.3624	3.5901	-1.3489	2.7079	0.2272	-0.0401	0.1141	-0.1955	-0.0549	0.3355	-0.0076	-0.1376	-0.116	0.2661	0.0361	-0.019	0.2145	-0.059	0.265	18.8356	48.7614	110.3995
55	1.2467	0.2145	-0.0464	1.0462	0.2513	2.2096	0.0347	-0.1567	0.1556	0.1949	-0.1068	-0.0633	0.0855	0.1331	0.0829	0.2494	-0.0016	-0.0098	0.2236	-0.0322	0.269	28.8728	42.8059	108.4785
56	3.1487	0.4778	0.3155	4.2876	-0.1956	1.333	0.136	0.0577	0.0201	-0.3736	-0.1135	0.1316	-0.0762	-0.0203	-0.0229	0.2491	-0.0164	0.0038	0.1613	-0.0035	0.2384	25.7229	50.5375	103.0078
57	2.8244	-0.1919	-0.7063	5.3949	4.073	7.2986	0.0367	0.0644	0.4617	-0.5144	0.2228	-0.4763	-0.5198	0.7091	-0.1199	0.272	-0.0413	0.0336	0.2083	0.0543	0.332	33.3204	47.5049	100.7299
58	3.6153	-0.299	-1.7212	1.7016	0.3211	3.1376	0.4379	-0.7285	0.2889	0.3116	-0.2983	-0.171	-0.1154	0.6196	-0.0954	0.2876	-0.067	0.0242	0.4036	-0.0223	0.385	55.2212	2.437	135.0412
59	0.8348	-0.3045	0.6244	0.3686	0.2243	1.3056	0.1089	0.2085	0.0312	-0.2494	-0.0527	-0.2434	0.4533	0.0891	-0.0443	0.2685	0.0206	-0.0149	0.2558	0.0287	0.3237	50.3437	-8.529	123.071
60	3.3823	0.205	0.0621	6.6874	-1.1061	4.1366	0.1709	0.3359	-0.2372	-0.0272	0.2219	0.397	0.4565	-0.1297	-0.2325	0.3783	0.0045	-0.053	0.3138	0.0085	0.3624	40.5516	-7.8413	116.26
61	2.5625	1.7802	0.5035	4.1617	0.4906	1.6991	0.2015	-0.194	0.0053	-0.0907	-0.1556	0.6244	-0.1408	-0.2729	-0.1206	0.2854	-0.0395	-0.024	0.3899	0.044	0.4287	9.1683	9.1219	117.1118
62	0.0477	0.0549	0.2474	1.8479	-0.276	1.5812	0.3069	0.0075	-0.256	-0.67	-0.0593	0.3655	0.3938	-0.3793	-0.1488	0.4879	-0.0907	-0.1137	0.3241	0.0151	0.3256	18.3485	-3.1119	109.4275
63	4.1795	0.4808	-0.9295	4.4207	-1.0703	6.2546	0.3069	0.3222	0.0763	-0.6832	-0.0619	-0.3183	0.0811	0.136	-0.0916	0.4645	0.0677	-0.0164	0.3759	0.0545	0.349	28.7662	-7.6016	113.3053
64	0.8983	0.8969	0.47	3.2374	1.7343	1.8651	-0.1025	0.1429	-0.0387	-0.3408	0.3346	-0.2766	-0.5881	0.461	-0.1996	0.3725	-0.1189	0.0563	0.3361	-0.0455	0.2494	18.3939	15.0623	70.1445
65	1.1696	0.6347	0.097	2.7096	-1.1879	2.3462	0.0716	0.0773	0.1415	0.2347	0.2312	0.2855	-0.6779	-0.4913	-0.2124	0.3209	0.0115	0.0313	0.2218	0.0069	0.2003	2.3133	15.9794	83.9114
66	7.4305	2.1822	-0.7388	5.277	-1.2197	2.1128	-0.0584	-0.1261	0.3029	0.1646	0.1833	0.1517	0.2	-0.512	-0.0419	0.7255	-0.0477	-0.0597	0.5465	0.0508	0.5087	-7.416	3.7142	92.5393
67	1.123	0.1098	-0.0205	1.4925	-0.2201	1.208	-0.034	0.0151	-0.0373	-0.2089	-0.0452	-0.114	0.1291	0.0839	0.079	0.2232	0.0078	0.0483	0.2188	0.0051	0.1965	30.2487	27.4753	100.0499
68	2.0098	-2.22	-0.7911	2.4475	0.8741	0.3124	0.3001	0.1972	0.3666	0.2445	0.2117	0.376	-0.4181	-0.7262	-0.2221	0.7607	0.1592	-0.0083	0.7152	-0.0079	0.4504	9.3796	41.8883	106.929

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 0 THROUGH 17 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 18 THROUGH 28 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 29 THROUGH 36 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 37 THROUGH 62 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 63 THROUGH 71 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 72 THROUGH 93 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 94 THROUGH 114 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 115 THROUGH 124 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 125 THROUGH 132 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 0 THROUGH 12 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 13 THROUGH 28 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 29 THROUGH 36 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 37 THROUGH 42 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 43 THROUGH 62 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 63 THROUGH 71 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 72 THROUGH 86 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 87 THROUGH 93 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 94 THROUGH 114 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 115 THROUGH 124 )
20	X-RAY DIFFRACTION	20	CHAIN 'B' AND (RESID 125 THROUGH 132 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 0 THROUGH 12 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 13 THROUGH 28 )
23	X-RAY DIFFRACTION	23	CHAIN 'C' AND (RESID 29 THROUGH 36 )
24	X-RAY DIFFRACTION	24	CHAIN 'C' AND (RESID 37 THROUGH 42 )
25	X-RAY DIFFRACTION	25	CHAIN 'C' AND (RESID 43 THROUGH 49 )
26	X-RAY DIFFRACTION	26	CHAIN 'C' AND (RESID 50 THROUGH 62 )
27	X-RAY DIFFRACTION	27	CHAIN 'C' AND (RESID 63 THROUGH 71 )
28	X-RAY DIFFRACTION	28	CHAIN 'C' AND (RESID 72 THROUGH 93 )
29	X-RAY DIFFRACTION	29	CHAIN 'C' AND (RESID 94 THROUGH 114 )
30	X-RAY DIFFRACTION	30	CHAIN 'C' AND (RESID 115 THROUGH 124 )
31	X-RAY DIFFRACTION	31	CHAIN 'C' AND (RESID 125 THROUGH 132 )
32	X-RAY DIFFRACTION	32	CHAIN 'D' AND (RESID 0 THROUGH 12 )
33	X-RAY DIFFRACTION	33	CHAIN 'D' AND (RESID 13 THROUGH 28 )
34	X-RAY DIFFRACTION	34	CHAIN 'D' AND (RESID 29 THROUGH 62 )
35	X-RAY DIFFRACTION	35	CHAIN 'D' AND (RESID 63 THROUGH 71 )
36	X-RAY DIFFRACTION	36	CHAIN 'D' AND (RESID 72 THROUGH 93 )
37	X-RAY DIFFRACTION	37	CHAIN 'D' AND (RESID 94 THROUGH 124 )
38	X-RAY DIFFRACTION	38	CHAIN 'D' AND (RESID 125 THROUGH 132 )
39	X-RAY DIFFRACTION	39	CHAIN 'E' AND (RESID 0 THROUGH 12 )
40	X-RAY DIFFRACTION	40	CHAIN 'E' AND (RESID 13 THROUGH 28 )
41	X-RAY DIFFRACTION	41	CHAIN 'E' AND (RESID 29 THROUGH 49 )
42	X-RAY DIFFRACTION	42	CHAIN 'E' AND (RESID 50 THROUGH 62 )
43	X-RAY DIFFRACTION	43	CHAIN 'E' AND (RESID 63 THROUGH 71 )
44	X-RAY DIFFRACTION	44	CHAIN 'E' AND (RESID 72 THROUGH 93 )
45	X-RAY DIFFRACTION	45	CHAIN 'E' AND (RESID 94 THROUGH 114 )
46	X-RAY DIFFRACTION	46	CHAIN 'E' AND (RESID 115 THROUGH 124 )
47	X-RAY DIFFRACTION	47	CHAIN 'E' AND (RESID 125 THROUGH 132 )
48	X-RAY DIFFRACTION	48	CHAIN 'F' AND (RESID 0 THROUGH 12 )
49	X-RAY DIFFRACTION	49	CHAIN 'F' AND (RESID 13 THROUGH 28 )
50	X-RAY DIFFRACTION	50	CHAIN 'F' AND (RESID 29 THROUGH 36 )
51	X-RAY DIFFRACTION	51	CHAIN 'F' AND (RESID 37 THROUGH 42 )
52	X-RAY DIFFRACTION	52	CHAIN 'F' AND (RESID 43 THROUGH 62 )
53	X-RAY DIFFRACTION	53	CHAIN 'F' AND (RESID 63 THROUGH 71 )
54	X-RAY DIFFRACTION	54	CHAIN 'F' AND (RESID 72 THROUGH 93 )
55	X-RAY DIFFRACTION	55	CHAIN 'F' AND (RESID 94 THROUGH 114 )
56	X-RAY DIFFRACTION	56	CHAIN 'F' AND (RESID 115 THROUGH 124 )
57	X-RAY DIFFRACTION	57	CHAIN 'F' AND (RESID 125 THROUGH 132 )
58	X-RAY DIFFRACTION	58	CHAIN 'G' AND (RESID 41 THROUGH 54 )
59	X-RAY DIFFRACTION	59	CHAIN 'G' AND (RESID 55 THROUGH 62 )
60	X-RAY DIFFRACTION	60	CHAIN 'G' AND (RESID 63 THROUGH 69 )
61	X-RAY DIFFRACTION	61	CHAIN 'H' AND (RESID 41 THROUGH 54 )
62	X-RAY DIFFRACTION	62	CHAIN 'H' AND (RESID 55 THROUGH 62 )
63	X-RAY DIFFRACTION	63	CHAIN 'H' AND (RESID 63 THROUGH 69 )
64	X-RAY DIFFRACTION	64	CHAIN 'I' AND (RESID 41 THROUGH 54 )
65	X-RAY DIFFRACTION	65	CHAIN 'I' AND (RESID 55 THROUGH 70 )
66	X-RAY DIFFRACTION	66	CHAIN 'I' AND (RESID 71 THROUGH 76)
67	X-RAY DIFFRACTION	67	CHAIN 'J' AND (RESID 41 THROUGH 70 )
68	X-RAY DIFFRACTION	68	CHAIN 'J' AND (RESID 71 THROUGH 76 )

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Movie

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Structure viewers

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Validation report

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Assembly

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Data collection

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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

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Yorodumi