PDB-5yei: Mechanistic insight into the regulation of Pseudomonas aeruginosa...

ID or keywords:

Entry

Database: PDB / ID: 5yei

Title

Mechanistic insight into the regulation of Pseudomonas aeruginosa aspartate kinase

Components

(Aspartokinase) x 2

Keywords

TRANSFERASE / Pseudomonas aeruginosa / aspartate kinase

Function / homology

Function and homology information

aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.301 Å

Authors

Li, C. / Yang, M. / Liu, L. / Peng, C. / Li, T. / He, L. / Song, Y. / Zhu, Y. / Bao, R.

Citation

Journal: Biochem.J. / Year: 2018
Title: Mechanistic insights into the allosteric regulation of Pseudomonas aeruginosa aspartate kinase.
Authors: Li, C. / Yang, M. / Liu, L. / Li, T. / Peng, C. / He, L. / Song, Y. / Zhu, Y. / Shen, Y. / Yang, J. / Zhao, N. / Zhao, C. / Zhou, Q. / Li, H. / Kang, M. / Tong, A. / Tang, H. / Bao, R.

History

Deposition	Sep 17, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 29, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 11, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2	Nov 22, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5yei.cif.gz	833.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5yei.ent.gz	697.4 KB	Display	PDB format
PDBx/mmJSON format	5yei.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5yei_validation.pdf.gz	545.8 KB	Display	wwPDB validaton report
Full document	5yei_full_validation.pdf.gz	621.4 KB	Display
Data in XML	5yei_validation.xml.gz	85.7 KB	Display
Data in CIF	5yei_validation.cif.gz	115.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ye/5yei ftp://data.pdbj.org/pub/pdb/validation_reports/ye/5yei	HTTPS FTP

-
Related structure data

Related structure data	3aawS S: Starting model for refinement
Similar structure data	2x6s-d 2x6n-d 2x74-d 4nh0-1 4nh0-2 4hre-1 1q7m-d 5lp4-d 4hre-2 1q7q-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#61 - Jan 2005 Phenylalanine Hydroxylase similarity (3) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (3)

Deposited unit

D: Aspartokinase

B: Aspartokinase

F: Aspartokinase

C: Aspartokinase

H: Aspartokinase

G: Aspartokinase

A: Aspartokinase

E: Aspartokinase

hetero molecules

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

1

D: Aspartokinase

B: Aspartokinase

C: Aspartokinase

A: Aspartokinase

hetero molecules

defined by author&software
Evidence: gel filtration
125 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Aspartokinase

H: Aspartokinase

G: Aspartokinase

E: Aspartokinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.459, 171.793, 88.932
Angle α, β, γ (deg.)	90.00, 90.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 2 types, 8 molecules DBFHCGAE

#1: Protein	Aspartokinase / Aspartate kinase Mass: 17750.230 Da / Num. of mol.: 4 / Fragment: UNP residues 249-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lysC, PA0904 / Plasmid: pET-22b (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O69077, aspartate kinase
#2: Protein	Aspartokinase / Aspartate kinase Mass: 44437.629 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lysC, PA0904 / Plasmid: pET-22b (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O69077, aspartate kinase

#1: Protein

Aspartokinase / Aspartate kinase

Mass: 17750.230 Da / Num. of mol.: 4 / Fragment: UNP residues 249-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lysC, PA0904 / Plasmid: pET-22b (+) / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O69077, aspartate kinase

#2: Protein

Aspartokinase / Aspartate kinase

Mass: 44437.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lysC, PA0904 / Plasmid: pET-22b (+) / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O69077, aspartate kinase

-
Non-polymers , 4 types, 191 molecules

#3: Chemical	ChemComp-THR / THREONINE Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Formula: C₄H₉NO₃
#4: Chemical	ChemComp-LYS / LYSINE Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₆H₁₅N₂O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.43 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.4 M ammonium sulfate 0.1 M sodium citrate tribasic dihydrate pH 5.6 0.9 M lithium sulfate monohydrate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97776 Å / Relative weight: 1
Reflection	Resolution: 2.3→40.9 Å / Num. obs: 106886 / % possible obs: 97.7 % / Redundancy: 3.8 % / R_sym value: 0.08 / Net I/σ(I): 7.52
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.94 / R_sym value: 0.665 / % possible all: 91.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.10.1-2155_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3AAW

3aaw

Resolution: 2.301→40.091 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2574	5272	4.93 %
R_work	0.2222	-	-
obs	0.2239	106872	97.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.301→40.091 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16651	0	122	176	16949

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	16957
X-RAY DIFFRACTION	f_angle_d	1.715	22959
X-RAY DIFFRACTION	f_dihedral_angle_d	23.615	6210
X-RAY DIFFRACTION	f_chiral_restr	0.129	2822
X-RAY DIFFRACTION	f_plane_restr	0.01	2961

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 (%)
2.301-2.3272	0.3682	150	0.326	2912	X-RAY DIFFRACTION	83
2.3272-2.3545	0.39	199	0.3278	3301	X-RAY DIFFRACTION	96
2.3545-2.3832	0.3715	178	0.319	3294	X-RAY DIFFRACTION	96
2.3832-2.4134	0.3313	173	0.3072	3364	X-RAY DIFFRACTION	97
2.4134-2.4452	0.3326	186	0.305	3321	X-RAY DIFFRACTION	97
2.4452-2.4787	0.3481	175	0.2968	3374	X-RAY DIFFRACTION	98
2.4787-2.5141	0.3569	154	0.2969	3355	X-RAY DIFFRACTION	97
2.5141-2.5516	0.3184	150	0.2936	3368	X-RAY DIFFRACTION	97
2.5516-2.5914	0.3037	188	0.2789	3381	X-RAY DIFFRACTION	98
2.5914-2.6339	0.3304	182	0.2765	3374	X-RAY DIFFRACTION	98
2.6339-2.6793	0.3295	177	0.2635	3380	X-RAY DIFFRACTION	98
2.6793-2.728	0.3074	148	0.2596	3396	X-RAY DIFFRACTION	97
2.728-2.7805	0.2849	181	0.2692	3350	X-RAY DIFFRACTION	97
2.7805-2.8372	0.3458	212	0.2705	3350	X-RAY DIFFRACTION	98
2.8372-2.8989	0.3111	153	0.2731	3375	X-RAY DIFFRACTION	98
2.8989-2.9663	0.307	232	0.2602	3402	X-RAY DIFFRACTION	98
2.9663-3.0405	0.2975	184	0.2475	3366	X-RAY DIFFRACTION	99
3.0405-3.1227	0.2465	181	0.2433	3391	X-RAY DIFFRACTION	99
3.1227-3.2145	0.283	138	0.234	3470	X-RAY DIFFRACTION	99
3.2145-3.3182	0.2847	184	0.2358	3399	X-RAY DIFFRACTION	99
3.3182-3.4368	0.2501	158	0.2208	3493	X-RAY DIFFRACTION	99
3.4368-3.5743	0.2319	145	0.2151	3488	X-RAY DIFFRACTION	99
3.5743-3.7368	0.253	135	0.206	3453	X-RAY DIFFRACTION	99
3.7368-3.9337	0.2162	149	0.2038	3463	X-RAY DIFFRACTION	99
3.9337-4.1799	0.2375	175	0.1881	3467	X-RAY DIFFRACTION	99
4.1799-4.5022	0.1839	199	0.1633	3437	X-RAY DIFFRACTION	100
4.5022-4.9546	0.1992	182	0.1641	3452	X-RAY DIFFRACTION	100
4.9546-5.6698	0.2431	169	0.1851	3481	X-RAY DIFFRACTION	100
5.6698-7.1368	0.2402	209	0.2178	3460	X-RAY DIFFRACTION	100
7.1368-40.0967	0.2003	226	0.176	3483	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	2.0001	2.0001	2.0002	2.0001	1.9999	2.0001	-0.3721	0.0988	0.6556	-0.2117	0.0458	0.2674	-0.6299	-0.0107	0.3204	0.4512	0.4127	0.2004	0.2218	0.1321	0.806	39.7393	9.5024	49.7936
2	2.0007	1.9993	1.9998	2	2.0003	1.9997	0.0364	0.3974	-0.6136	0.0003	0.2083	-0.2288	-0.699	0.579	-0.3673	0.4775	-0.1836	0.0251	0.3372	-0.1035	0.5295	46.4741	-8.0431	69.2402
3	2.0002	1.9997	1.9998	1.9998	-4.7828	1.9998	0.395	0.5161	-0.0223	0.7135	-0.2385	-0.3238	-0.5228	0.5506	-0.1825	0.4123	0.3162	-0.0512	0.6119	-0.1439	0.4549	56.7076	-78.0257	-21.4763
4	0.7426	-2.8555	-1.5038	2	5.1289	3.0757	0.0154	0.0589	-0.0744	-0.0048	-0.0196	0.0909	-0.0015	-0.0037	-0.0041	0.3103	-0.0708	-0.031	0.3325	0.0091	0.3592	12.0357	-2.2347	62.1191
5	7.3647	1.9999	9.6465	2.0001	1.9995	2.0003	0.1042	-0.0573	-0.0275	0.0203	-0.0762	0.2017	0.1486	-0.0458	-0.0376	0.5693	-0.111	-0.1031	0.4109	-0.0588	0.2862	11.511	-73.2274	-17.7483
6	8.6236	-4.6413	-9.045	4.6686	8.1801	2	0.1097	0.0612	0.0409	-0.0702	-0.0609	0.0236	0.1332	0.1312	-0.0347	0.2157	-0.0408	0.4274	0.0654	0.7324	-0.6054	44.7517	-66.905	-22.5371
7	1.9999	-2.8543	1.9998	1.9997	-5.9311	2.0001	0.0188	-0.2785	-0.1403	-0.1715	-0.0661	-0.2092	0.305	0.4149	0.0392	0.2619	-0.0451	-0.0228	0.5106	0.0312	0.3238	57.5233	2.379	66.0947
8	2	5.884	-9.3349	1.9999	2.0001	1.9999	0.1697	0.0277	0.2019	0.1148	0.138	-0.5422	-0.0126	0.1579	-0.2851	0.7657	-0.273	-0.2043	0.3633	0.2071	0.7593	18.2157	-22.6611	75.8256
9	2.0003	1.9999	-4.8761	2.0007	2.0009	2.0002	0.0807	0.2191	0.1409	-0.3512	0.0814	0.729	0.1067	-0.2928	-0.1824	0.4001	0.0958	0.1118	0.4849	0.1286	0.4656	0.0992	-5.6398	72.7741
10	2.0001	-8.7057	7.692	2.0001	3.2125	2.0001	-0.1082	0.1239	0.0126	-0.2059	0.2677	-0.7081	-0.3068	0.4746	-0.1347	0.7219	-0.049	0.2672	0.4585	0.1706	0.7039	17.0617	-52.8847	-31.5014
11	1.9999	-2.503	-2.0484	2.0005	2.9662	2.0002	0.308	0.076	0.143	0.5418	0.0711	0.8417	-0.5044	-0.4593	-0.3508	0.3822	-0.0889	0.0146	0.4033	-0.0682	0.5062	-0.6331	-69.8546	-28.2453
12	2.0001	1.9995	1.9999	1.9996	1.9997	2.0001	-0.0787	0.0347	-0.2561	0.1195	-0.0374	0.309	0.0875	-0.2929	0.1118	0.362	-0.1223	0.0578	0.5807	0.0744	0.236	38.8119	-84.8707	-5.3981
13	0.0155	0.002	0.013	0.0194	-0.0165	0.0094	0.0688	-0.1586	-0.2189	0.0615	0.2255	-0.1027	-0.2026	-0.2103	0	0.4141	-0.0246	0.0831	0.5231	-0.0474	0.3684	32.5207	-6.491	52.2448
14	0.4489	-0.2337	-0.194	0.3162	-0.0525	0.1663	0.0537	-0.0661	0.0965	-0.0382	-0.0049	0.0442	0.0347	-0.104	0.0011	0.2021	0.0055	0.0088	0.2369	-0.0013	0.1558	43.9207	3.0553	63.1543
15	0.0189	-0.0005	0.1059	0.0265	0.0581	0.1155	-0.0682	-0.3154	0.0949	-0.03	0.0597	0.0626	-0.0383	-0.1123	0.0056	0.2038	0.0034	0.0243	0.3524	-0.0148	0.1694	33.513	-1.8981	50.7626
16	0.0184	0.0357	-0.0226	0.0414	-0.0365	0.0222	-0.0834	0.3139	0.0262	-0.0346	-0.0059	0.07	0.0803	-0.0158	0	0.3884	0.0271	-0.0663	0.3615	-0.0253	0.2645	31.7976	-68.7015	-7.817
17	0.0037	0.0019	-0.0034	0.0394	-0.017	-0.0144	0.1912	0.0229	0.0222	-0.1538	-0.1308	-0.0039	-0.1708	0.0803	-0	0.3479	-0.0123	-0.0084	0.3162	-0.0309	0.281	49.8824	-82.7778	-22.8284
18	0.0355	0.0263	0.0211	0.0169	-0.0239	-0.012	0.176	-0.0471	0.0773	-0.0789	0.0057	-0.0838	0.117	-0.2156	0	0.2926	0.0066	0.023	0.3003	0.0084	0.2199	46.8845	-73.2137	-26.3712
19	0.1755	0.233	-0.1128	0.2321	0.1691	0.1663	-0.0205	0.0831	-0.0559	-0.0155	0.0195	0.0886	0.0477	-0.0601	0.0015	0.2155	0.0334	-0.0197	0.3029	-0.0374	0.1947	42.7385	-80.3553	-22.7354
20	0.0083	-0.0122	-0.0079	0.0072	0.0129	0.0008	0.1461	-0.0756	-0.0109	-0.0643	-0.0116	-0.0143	-0.0914	-0.1768	-0	0.2623	-0.0176	0.0417	0.3508	-0.0108	0.1842	38.6736	-73.7957	1.026
21	-0.0031	-0.0175	-0.0269	0.0184	-0.0334	0.0442	-0.2157	0.0295	-0.025	-0.1003	-0.0202	-0.1183	0.0111	0.0241	-0.0477	0.2591	-0.0823	-0.0017	0.215	-0.0007	0.1387	38.5219	-76.9501	-7.6718
22	0.0247	-0.0393	-0.0175	0.0076	0.022	0.002	-0.1008	0.2906	0.047	0.0331	0.054	0.0963	0.228	-0.362	-0	0.2833	-0.0088	0.0223	0.4932	-0.043	0.3337	29.5965	-73.9394	-5.8459
23	0.0112	0.001	-0.0048	-0.0046	0.0153	0.006	-0.3047	0.0118	-0.0472	0.0309	-0.1112	-0.0144	-0.0259	-0.0814	-0	0.3498	-0.033	0.0162	0.6618	-0.2247	0.6018	23.5444	-57.192	-13.8332
24	0.0482	-0.0179	0.0036	0.017	0.0791	0.0097	0.0271	0.3945	-0.1723	-0.1419	0.1053	0.1168	0.1319	0.227	0	0.236	0.0083	0.0442	0.4101	-0.0256	0.2981	8.9232	-73.635	-28.7602
25	0.0845	0.0766	-0.061	0.0657	0.0921	0.0684	-0.2276	0.1097	0.106	0.1058	0.0899	-0.0864	-0.0927	-0.1341	-0	0.2044	0.0333	0.0019	0.3261	0.0002	0.3192	9.1881	-68.6554	-28.0498
26	0.0597	-0.0156	-0.0789	0.0379	0.0589	0.1024	0.04	0.082	-0.149	-0.1053	-0.0893	-0.0518	0.0958	0.0801	-0.0336	0.2433	0.0061	0.0316	0.3593	-0.0694	0.2554	15.0308	-76.343	-33.9934
27	0.0367	-0.0118	0.0928	0.0223	0.0182	0.0209	0.0852	0.0137	0.1655	0.0815	0.0912	-0.1428	-0.333	0.1435	-0.0042	0.4691	-0.0891	0.0903	0.3317	-0.0064	0.5766	18.9243	-52.323	-21.1561
28	0.0054	0.0053	-0.0069	-0.0152	-0.003	0.0098	-0.1637	0.1594	0.0657	0.1787	-0.059	0.1443	0.0863	0.0414	-0	0.2003	0.0185	-0.0055	0.3756	-0.0247	0.3998	12.2306	-58.6737	-18.7935
29	0.0121	-0.0005	-0.0012	0.0348	-0.0423	-0.0157	-0.0972	-0.0041	-0.1014	0.0218	0.3655	-0.3235	-0.0069	0.4744	0.0004	0.3217	-0.1188	0.0915	0.5535	-0.1154	0.5806	26.2324	-55.4022	-22.2041
30	0.0814	0.1088	0.357	0.1783	0.1317	0.5632	0.1373	-0.0013	-0.0563	-0.0036	0.0214	-0.1225	0.1447	0.0526	0.0981	0.2619	0.0154	-0.0424	0.2029	-0.0796	0.3543	46.9787	-35.6831	35.0245
31	0.055	-0.0055	0.0874	0.1274	0.0864	-0.047	0.134	-0.0485	0.0387	0.0873	-0.1095	-0.0258	-0.0472	-0.151	0.001	0.3357	0.0056	-0.0593	0.349	-0.05	0.3712	50.8075	-25.6668	51.5176
32	0.518	-0.029	0.3042	0.3358	0.0006	0.2433	0.0125	0.0955	-0.018	0.0035	0.0281	-0.0203	-0.03	-0.0141	0.0112	0.146	0.0058	0.0152	0.1753	0.0077	0.1521	53.4814	-2.3977	54.4062
33	0.0424	0.0985	0.0794	0.103	-0.044	0.1147	0.0159	-0.0022	-0.1986	0.0318	0.0499	-0.0322	0.0266	-0.0456	0.0063	0.248	0.0201	-0.0074	0.379	-0.0577	0.3554	16.4914	-11.2314	68.2276
34	0.4036	-0.0732	0.289	0.3698	-0.1333	0.4427	0.0682	-0.3126	-0.1	-0.045	0.0557	-0.0989	0.1034	0.1221	0.0061	0.1975	0.01	-0.0317	0.2987	-0.0277	0.3157	14.5632	-9.1639	71.0996
35	0.0361	-0.0343	0.0277	0.0011	0.0011	0.0017	-0.5735	0.0416	-0.0357	-0.054	-0.114	-0.4051	-0.0801	-0.0513	-0.0363	-0.5463	1.011	-0.0154	-0.3706	-0.1889	0.7466	27.3638	-19.952	65.0688
36	0.1054	-0.1101	0.0683	0.6205	0.3723	0.2689	0.0905	-0.0489	0.0928	-0.0414	-0.0941	0.0465	-0.0875	-0.1602	0.0333	0.2918	0.045	0.0062	0.2955	-0.0458	0.2415	10.9966	-27.6713	26.4122
37	0.0861	-0.0469	-0.088	0.025	0.1121	0.0815	0.1367	-0.0476	0.0275	-0.0266	-0.1326	-0.0684	-0.1696	-0.1771	-0	0.3217	0.0488	0.0059	0.3825	-0.0485	0.2883	4.8867	-11.8916	42.0612
38	0.0548	0.0392	-0.0094	0.0164	-0.0008	0.0246	0.1753	0.1647	-0.1032	0.086	-0.0765	0.0506	-0.0522	-0.0961	-0	0.6198	0.0995	0.0197	0.4529	-0.114	0.393	10.2211	-14.5969	37.2148
39	0.3575	-0.1103	-0.1127	0.4535	0.232	0.3504	0.045	-0.0553	-0.0872	0.049	0.0019	-0.0841	0.1046	-0.1268	-0.0016	0.1911	-0.004	-0.0362	0.1396	0.0201	0.2211	4.4211	-15.8721	65.5445
40	0.1118	0.0525	-0.2248	-0.0473	-0.0465	0.3886	0.059	0.0389	0.0035	0.0414	0.1274	-0.1117	-0.016	0.0455	0.0902	0.3122	0.008	0.0148	0.2903	-0.0968	0.4161	46.7453	-39.8015	9.3583
41	0.1319	-0.0691	-0.1314	0.087	0.0689	-0.0511	0.1858	-0.2131	0.0089	-0.0529	-0.2011	-0.0395	0.0123	0.0298	0	0.3417	0.0022	0.0998	0.3152	-0.0458	0.3208	50.3593	-49.814	-7.1916
42	0.5668	-0.1148	-0.2505	0.3999	-0.091	0.1539	0.0211	-0.0316	-0.0376	0.0256	-0.0013	-0.1023	-0.0036	-0.0281	0.0042	0.1018	0.0096	-0.0099	0.111	-0.0101	0.0719	52.6126	-73.0442	-9.8812
43	0.0514	0.0387	-0.1703	0.5169	0.3131	0.3063	0.037	0.0885	-0.1081	-0.0451	-0.0105	0.0012	0.0411	-0.2181	0.2381	0.2944	-0.0484	-0.0183	0.3015	-0.045	0.2535	10.8197	-47.6233	17.9824
44	0.0521	-0.0277	0.0092	0.245	0.1031	0.0038	-0.0565	0.0235	-0.0711	-0.0403	-0.0212	-0.0865	-0.15	-0.1293	-0.0413	0.2548	-0.0587	0.0234	0.2556	-0.0834	0.1919	4.477	-63.5409	2.2921
45	0.0183	-0.0037	0.0856	0.0714	-0.0149	0.0377	-0.1006	-0.1603	-0.0209	-0.3088	0.082	0.2524	-0.0504	-0.1386	0	0.6404	-0.1013	0.0364	0.4298	-0.0951	0.3053	9.9044	-60.7065	7.2654
46	0.5966	0.1615	0.0951	0.4211	-0.0055	0.4198	-0.0347	0.01	0.2221	-0.0634	0.0278	-0.0835	-0.0746	-0.0772	-0.0025	0.2399	-0.0119	0.023	0.194	-0.001	0.2859	3.3901	-59.5875	-21.0597

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 250 through 263 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 264 through 373 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 374 through 405 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 250 through 263 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 264 through 276 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 277 through 297 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 298 through 350 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 351 through 367 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 368 through 380 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 381 through 405 )
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 253 through 260 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 261 through 288 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 289 through 312 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 313 through 340 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 341 through 373 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 374 through 380 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 381 through 403 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 2 through 183 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 184 through 237 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 238 through 406 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 250 through 276 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 277 through 380 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 381 through 405 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 2 through 163 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 164 through 212 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 213 through 237 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 238 through 406 )
28	X-RAY DIFFRACTION	28	chain 'A' and (resid 2 through 183 )
29	X-RAY DIFFRACTION	29	chain 'A' and (resid 184 through 237 )
30	X-RAY DIFFRACTION	30	chain 'A' and (resid 238 through 406 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 2 through 163 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 164 through 212 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 213 through 237 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 238 through 406 )

-
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://pdbjlvh1.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

-
Protein , 2 types, 8 molecules DBFHCGAE

-
Non-polymers , 4 types, 191 molecules

-
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

-Protein , 2 types, 8 molecules DBFHCGAE

-Non-polymers , 4 types, 191 molecules

-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

-
Protein , 2 types, 8 molecules DBFHCGAE

-
Non-polymers , 4 types, 191 molecules

-
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