PDB-7k34: Crystal structure of L-threonine transaldolase from Pseudomonas f...

ID or keywords:

Entry

Database: PDB / ID: 7k34

Title

Crystal structure of L-threonine transaldolase from Pseudomonas fluorescens in internal aldimine state

Components

Threonine aldolase

Keywords

BIOSYNTHETIC PROTEIN / SYNTHASE / threonine transaldolase / pyridoxal phosphate / PLP / biocatalysis

Function / homology

Function and homology information

L-threonine aldolase / threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / cobalt ion binding / folic acid metabolic process / one-carbon metabolic process ...
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 Å

Authors

Kumar, P. / Bingman, C.A. / Buller, A.R.

Funding support

United States, 1items

Citation

Journal: Acs Chem.Biol. / Year: 2021
Title: l-Threonine Transaldolase Activity Is Enabled by a Persistent Catalytic Intermediate.
Authors: Kumar, P. / Meza, A. / Ellis, J.M. / Carlson, G.A. / Bingman, C.A. / Buller, A.R.

History

Deposition	Sep 10, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 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
Revision 1.3	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7k34.cif.gz	648 KB	Display	PDBx/mmCIF format
PDB format	pdb7k34.ent.gz	518.1 KB	Display	PDB format
PDBx/mmJSON format	7k34.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7k34_validation.pdf.gz	468.8 KB	Display	wwPDB validaton report
Full document	7k34_full_validation.pdf.gz	476.5 KB	Display
Data in XML	7k34_validation.xml.gz	69 KB	Display
Data in CIF	7k34_validation.cif.gz	98.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k3/7k34 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/7k34	HTTPS FTP

-
Related structure data

Related structure data	4ot8S S: Starting model for refinement
Similar structure data	3dpy-d 3eu5-d 5l46-1 4q4k-d 1y8j-d 4l6h-d 5l46-2 6lds-1 5mtz-1 3f9t-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

Deposited unit

A: Threonine aldolase

B: Threonine aldolase

C: Threonine aldolase

D: Threonine aldolase

hetero molecules

202 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Threonine aldolase

B: Threonine aldolase

hetero molecules

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

2

C: Threonine aldolase

D: Threonine aldolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	118.613, 118.613, 129.976
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	Threonine aldolase Mass: 50244.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: obiH, CIB54_12585 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1X9LWZ7, L-threonine aldolase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.93 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: N-His-ObiH at 30 mg/ml was dissolved in 10 mM Tris pH 8.5. Two microliter of protein solution was mixed with two microliter of reservoir solution, 0.1 M Bis-Tris pH 6.75 - 7.0, 1.8 - 2.0 M ...Details: N-His-ObiH at 30 mg/ml was dissolved in 10 mM Tris pH 8.5. Two microliter of protein solution was mixed with two microliter of reservoir solution, 0.1 M Bis-Tris pH 6.75 - 7.0, 1.8 - 2.0 M ammonium sulfate and equilibrated against the reservoir at 21 C (294K)

Crystal

Density Matthews: 2.27 Å³/Da / Density % sol: 45.93 %

Crystal grow

Temperature: 294 K / Method: vapor diffusion, sitting drop
Details: N-His-ObiH at 30 mg/ml was dissolved in 10 mM Tris pH 8.5. Two microliter of protein solution was mixed with two microliter of reservoir solution, 0.1 M Bis-Tris pH 6.75 - 7.0, 1.8 - 2.0 M ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 8, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03321 Å / Relative weight: 1
Reflection	Resolution: 1.66→118.6 Å / Num. obs: 211275 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.996 / R_pim(I) all: 0.083 / R_rim(I) all: 0.216 / Net I/σ(I): 6.9
Reflection shell	Resolution: 1.66→1.7 Å / Redundancy: 13.1 % / Num. unique obs: 15546 / CC_1/2: 0.45 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4OT8

4ot8

Resolution: 1.66→50.005 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.939 / WR_factor R_free: 0.247 / WR_factor R_work: 0.216 / SU B: 6.784 / SU ML: 0.109 / Average fsc free: 0.8546 / Average fsc work: 0.8673 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2423	10401	4.932 %	Random selection
R_work	0.2127	200497	-	-
all	0.214	-	-	-
obs	-	210898	99.849 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.211 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.239 Å²	-0 Å²	-0 Å²
2-	-	0.239 Å²	-0 Å²
3-	-	-	-0.477 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→50.005 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13407	0	45	919	14371

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	14007
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	12421
X-RAY DIFFRACTION	r_angle_refined_deg	1.269	1.63	19128
X-RAY DIFFRACTION	r_angle_other_deg	1.265	1.567	28781
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.493	5	1804
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.672	22.925	670
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.304	15	2063
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.902	15	59
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1809
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	16086
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2927
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	2986
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	11545
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	6748
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	5408
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.114	0.2	828
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.11	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.182	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	0.295	1.305	7156
X-RAY DIFFRACTION	r_mcbond_other	0.295	1.305	7155
X-RAY DIFFRACTION	r_mcangle_it	0.518	1.956	8971
X-RAY DIFFRACTION	r_mcangle_other	0.518	1.956	8972
X-RAY DIFFRACTION	r_scbond_it	0.303	1.349	6851
X-RAY DIFFRACTION	r_scbond_other	0.288	1.327	6815
X-RAY DIFFRACTION	r_scangle_it	0.488	2.012	10154
X-RAY DIFFRACTION	r_scangle_other	0.478	1.979	10100
X-RAY DIFFRACTION	r_lrange_it	4.632	16.346	15743
X-RAY DIFFRACTION	r_lrange_other	4.562	16.005	15602

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.66-1.703	0.342	790	0.326	14650	0.327	15523	0.635	0.645	99.4653	0.328
1.703-1.75	0.312	808	0.308	14299	0.308	15178	0.744	0.749	99.5322	0.307
1.75-1.801	0.298	712	0.293	14053	0.293	14808	0.778	0.784	99.7096	0.29
1.801-1.856	0.305	702	0.273	13645	0.274	14371	0.831	0.834	99.833	0.265
1.856-1.917	0.305	695	0.272	13140	0.274	13862	0.84	0.854	99.8052	0.263
1.917-1.984	0.293	632	0.253	12792	0.254	13443	0.853	0.882	99.8587	0.241
1.984-2.059	0.247	671	0.223	12282	0.224	12960	0.896	0.907	99.946	0.213
2.059-2.143	0.249	595	0.217	11905	0.219	12506	0.898	0.911	99.952	0.208
2.143-2.238	0.252	533	0.215	11468	0.217	12009	0.892	0.903	99.9334	0.207
2.238-2.347	0.304	575	0.241	10851	0.244	11444	0.866	0.897	99.8427	0.236
2.347-2.473	0.239	530	0.207	10413	0.209	10945	0.914	0.918	99.9817	0.204
2.473-2.623	0.232	514	0.195	9804	0.197	10318	0.923	0.933	100	0.196
2.623-2.803	0.242	466	0.2	9189	0.202	9655	0.914	0.93	100	0.203
2.803-3.027	0.247	456	0.203	8612	0.205	9068	0.909	0.928	100	0.209
3.027-3.315	0.211	396	0.2	7959	0.2	8355	0.932	0.937	100	0.209
3.315-3.704	0.216	389	0.197	7145	0.198	7535	0.935	0.94	99.9867	0.211
3.704-4.273	0.197	329	0.17	6329	0.171	6658	0.947	0.955	100	0.185
4.273-5.224	0.203	282	0.178	5372	0.179	5654	0.942	0.949	100	0.195
5.224-7.348	0.25	212	0.222	4210	0.224	4422	0.929	0.936	100	0.237
7.348-50.005	0.234	114	0.196	2379	0.197	2493	0.958	0.95	100	0.218

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	0.6134	-0.2836	-0.0329	0.7897	0.4246	0.6866	-0.0201	-0.0502	0.1619	0.0823	0.1479	-0.1667	0.0056	0.1074	-0.1278	0.1435	0.0079	-0.0186	0.1956	-0.0575	0.1242	35.311	-2.3032	-7.2274
2	3.2496	0.5015	-1.9972	1.95	0.0451	3.9033	-0.0413	0.0318	-0.2175	0.0863	-0.2121	0.1368	0.2001	-0.1612	0.2534	0.1049	-0.0145	-0.0214	0.1915	-0.0006	0.1094	13.5894	-11.8256	-17.3581
3	0.5021	0.0904	-0.2471	3.0563	0.2269	1.1589	-0.0405	0.0272	-0.0681	0.155	0.0128	-0.003	0.1711	0.1182	0.0277	0.134	0.0097	-0.0124	0.1612	-0.0212	0.0791	25.8563	-23.3972	-20.0255
4	3.1434	1.588	-1.586	4.0895	-1.1939	3.4553	0.0051	-0.0612	-0.0756	0.2838	0.0907	-0.3013	0.0298	0.2706	-0.0958	0.195	0.0814	-0.0556	0.1512	-0.0613	0.1024	38.6525	-32.65	-17.8352
5	1.1933	0.7631	-0.0656	1.5483	-0.4506	2.5962	-0.0131	0.096	-0.1476	0.1164	0.1691	-0.1216	0.3524	0.1964	-0.1559	0.1892	0.0753	-0.0206	0.176	-0.0954	0.0919	40.3523	-36.5889	-25.6105
6	1.7104	1.7636	-0.5235	4.484	-0.4034	0.5306	-0.0901	0.2492	-0.1933	-0.1279	0.1589	-0.2495	0.2137	0.0774	-0.0688	0.203	0.0609	-0.0205	0.2117	-0.0748	0.0972	37.2942	-32.4091	-27.4129
7	3.1548	1.5197	-0.7576	10.0037	-1.6766	6.5781	-0.0948	0.0698	-0.2588	0.0678	-0.0094	0.155	0.2323	-0.2184	0.1042	0.1886	0.0078	-0.0103	0.1799	-0.0707	0.1155	30.6486	-35.3516	-34.7062
8	0.7274	-0.0529	0.0155	1.0742	0.5276	0.765	0.0194	0.1431	-0.0031	-0.1024	0.0592	-0.0586	0.0106	0.089	-0.0786	0.1631	-0.0027	-0.0033	0.209	-0.0224	0.07	32.1834	-15.7074	-25.076
9	2.6619	-0.4847	-0.1346	2.0745	1.1632	1.875	-0.0058	0.0606	-0.0537	0.0822	0.4152	-0.5183	0.2447	0.4904	-0.4094	0.0431	0.0731	-0.0435	0.336	-0.2137	0.1825	55.5833	-19.6637	-21.5808
10	1.6859	-0.8974	-0.1634	1.3423	0.5335	0.9752	0.0536	0.0878	0.3269	-0.1349	0.1936	-0.4138	-0.1642	0.3284	-0.2472	0.0762	-0.0787	0.0684	0.2251	-0.0817	0.1541	47.2052	-1.2373	-20.896
11	1.092	0.5316	-0.6221	1.4914	-0.3264	2.0541	-0.0393	0.1258	0.2411	-0.1832	0.0933	0.0602	-0.07	-0.113	-0.054	0.1405	0.0123	0.0013	0.1445	0.0154	0.121	18.5675	1.9978	-14.2346
12	1.101	0.8004	-0.9686	0.7758	-0.0493	3.9117	0.0602	0.0063	0.0817	0.0333	0.1308	-0.0551	0.0952	0.1755	-0.1909	0.149	-0.0067	-0.0013	0.2391	-0.113	0.2027	37.1847	-8.1872	-6.5318
13	2.3871	2.8179	-4.9328	3.3438	-5.8507	10.2438	-0.0276	0.2749	0.157	-0.0947	0.3396	0.1588	0.2016	-0.5694	-0.312	0.55	0.1766	-0.1468	0.3656	-0.0668	0.2316	48.5387	-21.0517	-6.192
14	6.1011	1.5011	-5.8529	1.9762	-1.9454	6.8861	-0.0251	-0.2877	0.0066	0.3483	0.0876	-0.1963	0.0733	0.2457	-0.0625	0.1669	0.0772	-0.072	0.2016	-0.088	0.0674	40.2862	-10.3282	4.4337
15	1.2409	-0.0455	-1.1173	2.2008	-0.0254	1.1744	-0.2605	-0.003	-0.0906	0.2532	0.2453	0.2833	0.3996	0.0362	0.0152	0.3249	0.0726	-0.0034	0.1422	0.0252	0.0628	26.5187	-27.0401	1.3995
16	0.9105	-1.3648	-0.4717	8.3698	1.0329	6.0668	-0.1305	0.0763	-0.0453	-0.3033	0.0151	0.1201	-0.1817	0.0559	0.1154	0.2971	-0.0448	0.0407	0.0585	0.0467	0.1417	19.0564	-33.0359	-3.0585
17	1.2206	-1.7823	-1.7211	3.8997	1.5242	3.7909	-0.4439	-0.1411	-0.3801	1.1156	0.1424	0.6623	0.6352	0.0707	0.3015	0.7995	0.075	0.2732	0.1605	0.1924	0.3001	16.4807	-34.9386	11.6913
18	0.6796	-0.3854	-0.0693	1.4723	0.2135	0.4559	-0.1687	-0.2253	-0.0389	0.4528	0.1962	0.0443	0.277	0.0907	-0.0275	0.303	0.0937	-0.0023	0.1759	0.0109	0.0055	27.1554	-19.408	6.912
19	2.1105	-0.2567	-0.2795	1.0652	0.5882	1.1269	-0.149	-0.0772	-0.1087	0.2927	-0.0056	0.3283	0.2032	-0.1907	0.1546	0.1913	-0.0202	0.1104	0.1682	-0.0137	0.1092	5.0976	-10.0153	6.6862
20	2.4361	0.6226	-0.0165	1.4417	0.5799	0.7641	0.0653	-0.005	0.3818	0.1069	-0.0256	0.1773	-0.0511	-0.1177	-0.0397	0.1518	0.045	0.0161	0.1547	-0.0014	0.123	15.5608	4.5266	0.1078
21	2.4164	-1.9344	3.1634	3.388	-3.9181	8.1793	0.0734	0.1203	-0.0866	-0.1309	-0.0469	0.3167	0.1518	-0.1497	-0.0265	0.1257	-0.0105	-0.0322	0.137	-0.0597	0.1963	53.3622	-41.1957	14.2852
22	0.3893	-0.1156	-0.011	1.9482	-0.5235	0.8605	-0.0364	-0.0354	-0.014	0.0349	0.0195	0.1423	0.0451	-0.0091	0.0169	0.1697	-0.0081	-0.007	0.1659	-0.0121	0.0678	63.8115	-29.5887	29.7177
23	2.1552	-0.0174	2.8644	6.4067	-5.8831	9.174	-0.2324	0.2337	-0.0063	0.2587	0.0467	-0.1911	-0.5649	0.3033	0.1857	0.3239	-0.0992	0.0037	0.2923	-0.0569	0.262	75.5851	-8.8996	26.6219
24	1.3783	-0.6045	0.4042	0.8528	-0.1573	0.7255	-0.0151	0.0112	-0.026	0.0699	0.0497	-0.0256	0.0526	0.1452	-0.0345	0.18	-0.0122	-0.0174	0.1986	-0.0179	0.0693	77.6237	-25.9824	35.6972
25	8.0721	0.8444	-1.4223	5.9471	-2.7091	9.1714	0.0284	0.396	0.163	-0.0561	0.1547	0.3135	0.1293	0.1914	-0.1831	0.1436	0.052	-0.0178	0.2448	-0.0436	0.1156	90.7074	-35.2988	27.4652
26	1.6332	0.7192	-0.4869	1.6413	0.0006	1.2688	0.0288	-0.0101	-0.1116	0.2696	0.0597	-0.1875	0.2491	0.3272	-0.0885	0.1996	0.0987	-0.0951	0.2167	-0.0353	0.0524	90.2175	-39.4759	44.0617
27	10.6218	0.3162	-1.1648	1.6914	-0.9287	10.0104	-0.0071	0.1297	0.1679	0.0534	-0.126	-0.2872	-0.2065	0.3471	0.1331	0.1768	0.0135	-0.0886	0.2224	-0.0253	0.1183	92.756	-30.3971	49.7806
28	1.1432	0.0599	0.4644	0.7404	0.139	0.8245	-0.027	-0.038	0.0257	0.1173	0.048	-0.0139	0.0472	0.1051	-0.0209	0.1816	0.0053	-0.0216	0.1809	-0.005	0.062	75.111	-27.9788	37.9213
29	0.8786	-0.3838	-0.0887	2.1872	0.1373	0.8253	-0.0381	-0.0837	-0.179	0.254	0.0381	-0.1258	0.2289	0.071	-0	0.2365	0.0383	-0.0036	0.1202	0.0339	0.0653	70.969	-51.3568	40.2961
30	0.7644	-0.8074	0.0427	2.2844	-0.1242	0.6428	-0.0748	-0.0724	-0.2132	0.1479	0.0855	0.3166	0.2046	-0.1	-0.0107	0.1847	-0.053	0.0516	0.1265	0.021	0.1117	55.4746	-46.7355	36.1792
31	0.8361	0.3481	-0.4095	1.5246	-0.4563	2.032	0.0639	-0.1031	-0.0082	0.0951	-0.0608	0.26	-0.1952	-0.0963	-0.0031	0.1502	-0.0075	-0.0075	0.1636	-0.0112	0.116	55.0344	-18.3098	28.9756
32	0.2818	0.4286	-0.0949	1.9188	-0.3843	2.5517	-0.0949	-0.0663	-0.1315	-0.0655	0.022	-0.0229	0.2163	0.2226	0.073	0.2217	0.0177	0.0205	0.174	0.0155	0.1141	68.6812	-40.9314	20.6103
33	3.9058	-0.5942	1.5812	3.1265	-3.2977	5.1997	-0.106	-0.1921	-0.1224	0.1603	-0.1095	-0.1856	0.202	0.2378	0.2155	0.1836	0.0406	-0.0124	0.1126	-0.0231	0.1137	68.437	-46.1935	20.5325
34	3.1667	-0.2982	-0.1141	1.264	0.7779	2.2567	0.0165	0.0091	0.0215	-0.159	0.0418	-0.0675	-0.0383	0.1065	-0.0583	0.1761	0.0092	0.004	0.1705	0.0057	0.0631	77.3548	-33.0425	11.4781
35	2.6664	-1.1104	1.0018	1.6598	0.165	3.6431	-0.0641	-0.2986	-0.0071	-0.1065	0.2308	-0.265	-0.3283	0.2273	-0.1666	0.1602	-0.0969	0.0936	0.2274	-0.0557	0.1102	89.0216	-18.482	15.516
36	2.5016	-0.8287	0.5527	3.0776	0.7256	1.4335	0.0143	0.0717	0.0509	-0.6797	0.1719	-0.3858	-0.2891	0.4992	-0.1862	0.2994	-0.1227	0.1551	0.2793	-0.0596	0.0873	88.6922	-18.6303	2.6844
37	1.113	-0.4065	-0.3365	1.0237	0.3105	0.5827	0.0336	0.0694	-0.0462	-0.2016	-0.023	-0.0373	-0.0314	0.0702	-0.0105	0.2004	0.0059	-0.0002	0.1827	-0.0112	0.0537	73.3544	-29.8404	9.9401
38	1.0557	-0.0027	-0.0478	1.6077	0.7167	1.5851	0.102	0.0644	0.1846	-0.3294	-0.0366	-0.1155	-0.3943	0.1344	-0.0654	0.2967	-0.0226	0.0104	0.1024	0.0248	0.0479	68.1842	-5.4057	8.143
39	3.0022	-0.4032	-1.8187	0.9555	-1.0179	3.059	0.3577	0.1614	0.7174	-0.0724	0.0627	0.0227	-0.3922	-0.1644	-0.4204	0.4687	0.0315	-0.0994	0.0519	0.0879	0.3473	59.5547	3.5204	12.523
40	0.5494	0.2157	-0.1113	3.0885	-0.0068	0.5258	-0.0196	0.03	-0.063	-0.093	0.0269	0.3928	-0.1156	-0.2088	-0.0072	0.1458	0.0451	-0.0782	0.1591	-0.0264	0.1346	49.6896	-24.1048	14.3562

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 61
2	X-RAY DIFFRACTION	2	ALL	A	62 - 89
3	X-RAY DIFFRACTION	3	ALL	A	90 - 118
4	X-RAY DIFFRACTION	4	ALL	A	119 - 138
5	X-RAY DIFFRACTION	5	ALL	A	139 - 164
6	X-RAY DIFFRACTION	6	ALL	A	165 - 187
7	X-RAY DIFFRACTION	7	ALL	A	188 - 199
8	X-RAY DIFFRACTION	8	ALL	A	200 - 308
9	X-RAY DIFFRACTION	9	ALL	A	309 - 362
10	X-RAY DIFFRACTION	10	ALL	A	363 - 440
11	X-RAY DIFFRACTION	11	ALL	B	0 - 42
12	X-RAY DIFFRACTION	12	ALL	B	43 - 60
13	X-RAY DIFFRACTION	13	ALL	B	61 - 70
14	X-RAY DIFFRACTION	14	ALL	B	71 - 93
15	X-RAY DIFFRACTION	15	ALL	B	94 - 127
16	X-RAY DIFFRACTION	16	ALL	B	128 - 145
17	X-RAY DIFFRACTION	17	ALL	B	146 - 177
18	X-RAY DIFFRACTION	18	ALL	B	178 - 285
19	X-RAY DIFFRACTION	19	ALL	B	286 - 390
20	X-RAY DIFFRACTION	20	ALL	B	391 - 440
21	X-RAY DIFFRACTION	21	ALL	C	-1 - 30
22	X-RAY DIFFRACTION	22	ALL	C	31 - 60
23	X-RAY DIFFRACTION	23	ALL	C	61 - 70
24	X-RAY DIFFRACTION	24	ALL	C	71 - 130
25	X-RAY DIFFRACTION	25	ALL	C	131 - 143
26	X-RAY DIFFRACTION	26	ALL	C	144 - 188
27	X-RAY DIFFRACTION	27	ALL	C	189 - 199
28	X-RAY DIFFRACTION	28	ALL	C	200 - 282
29	X-RAY DIFFRACTION	29	ALL	C	283 - 376
30	X-RAY DIFFRACTION	30	ALL	C	377 - 440
31	X-RAY DIFFRACTION	31	ALL	D	0 - 42
32	X-RAY DIFFRACTION	32	ALL	D	43 - 67
33	X-RAY DIFFRACTION	33	ALL	D	68 - 81
34	X-RAY DIFFRACTION	34	ALL	D	82 - 118
35	X-RAY DIFFRACTION	35	ALL	D	119 - 143
36	X-RAY DIFFRACTION	36	ALL	D	144 - 200
37	X-RAY DIFFRACTION	37	ALL	D	201 - 288
38	X-RAY DIFFRACTION	38	ALL	D	289 - 381
39	X-RAY DIFFRACTION	39	ALL	D	382 - 405
40	X-RAY DIFFRACTION	40	ALL	D	406 - 440

-
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