PDB-2rjf: Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 1...

ID or keywords:

Entry

Database: PDB / ID: 2rjf

Title

Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 12-30), orthorhombic form I

Components

Histone H4
Lethal(3)malignant brain tumor-like protein

Keywords

TRANSCRIPTION / L(3)MBT-LIKE PROTEIN /

STRUCTURAL GENOMICS /

STRUCTURAL GENOMICS CONSORTIUM / SGC / Chromatin regulator / DNA-binding / Metal-binding /

Nucleus /

Repressor /

Transcription regulation /

Zinc-finger /

Chromosomal protein /

Methylation / Nucleosome core

Function / homology

Function and homology information

SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division /

hemopoiesis /

nucleosome binding / heterochromatin formation / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. ...

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2007
Title: L3MBTL1 recognition of mono- and dimethylated histones.
Authors: Min, J. / Allali-Hassani, A. / Nady, N. / Qi, C. / Ouyang, H. / Liu, Y. / MacKenzie, F. / Vedadi, M. / Arrowsmith, C.H.

History

Deposition	Oct 14, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 25, 2013	Group: Derived calculations
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2rjf.cif.gz	221.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2rjf.ent.gz	178.8 KB	Display	PDB format
PDBx/mmJSON format	2rjf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rj/2rjf ftp://data.pdbj.org/pub/pdb/validation_reports/rj/2rjf	HTTPS FTP

-
Related structure data

Related structure data	2pqwSC 2rjcC 2rjdC 2rjeC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6seh-d 3gvc-d 6mkb-d 3btc-d 3btj-d 4ina-d 3bt9-d 4b1v-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2pqwSC

2rjcC

2rjdC

2rjeC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lethal(3)malignant brain tumor-like protein

B: Histone H4

C: Lethal(3)malignant brain tumor-like protein

D: Histone H4

E: Lethal(3)malignant brain tumor-like protein

118 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lethal(3)malignant brain tumor-like protein

C: Lethal(3)malignant brain tumor-like protein

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

2

A: Lethal(3)malignant brain tumor-like protein

B: Histone H4

C: Lethal(3)malignant brain tumor-like protein

D: Histone H4

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

3

B: Histone H4

D: Histone H4

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

4

E: Lethal(3)malignant brain tumor-like protein

defined by author&software
37.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.458, 117.809, 132.316
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lethal(3)malignant brain tumor-like protein / L(3)mbt-like / L(3)mbt protein homolog / H-l(3)mbt protein / H-L(3)MBT / L3MBTL1 Mass: 37751.211 Da / Num. of mol.: 3 / Fragment: Residues 200-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pET28a-mhl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y468
#2: Protein/peptide	Histone H4 / Mass: 2344.763 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.99 Å³/Da / Density % sol: 58.85 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 5% PEG 4000, 0.1M Sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 10, 2007 / Details: varimax
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.05→39.65 Å / Num. all: 86421 / Num. obs: 86421 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / R_merge(I) obs: 0.082

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
CrystalClear		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2PQW

2pqw

Resolution: 2.05→39.65 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.941 / SU B: 8.027 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22533	4370	5.1 %	RANDOM
R_work	0.1791	-	-	-
all	0.18142	81955	-	-
obs	0.18142	81955	97.34 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 27.404 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0 Å²	0 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	0.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→39.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7840	0	0	573	8413

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.021	8140
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.727	1.926	11119
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.937	5	959
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.335	23.808	407
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.919	15	1205
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.206	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	1109
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6490
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	3193
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	5296
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	500
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.178	0.2	56
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.207	0.2	21
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.1	1.5	4965
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.656	2	7879
X-RAY DIFFRACTION	r_scbond_it	2.706	3	3749
X-RAY DIFFRACTION	r_scangle_it	4.09	4.5	3240
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.05→2.11 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	287	-
R_work	0.278	5618	-
obs	-	-	91.11 %

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	0.9572	1.5014	-0.4812	3.4619	-0.9549	0.9526	0.1146	-0.0598	0.0616	0.2007	-0.0421	0.2019	0.2272	-0.2909	-0.0725	0.1126	-0.1176	-0.0083	0.126	0.042	0.0315	-21.9429	38.3723	-9.3083
2	3.0382	0.1819	0.02	1.1583	-0.4006	2.3687	0.0325	0.2929	0.0509	-0.1398	0.0288	-0.0361	0.3432	-0.0156	-0.0613	0.1197	-0.0064	0.0043	0.044	0.02	0.0754	-7.7482	48.5316	-21.6858
3	4.1669	-0.2924	0.3767	1.0475	-0.1894	4.3487	0.0126	0.2786	0.3253	-0.1549	-0.0668	-0.0606	0.0115	0.2254	0.0542	0.0493	0.0188	0.0088	0.0743	0.0472	0.1394	2.46	55.3843	-17.5686
4	7.2278	-5.134	2.7681	13.7234	4.2935	12.403	0.1636	0.7669	0.9252	-0.1617	-0.124	-1.4097	-0.043	1.234	-0.0395	-0.0486	-0.0526	0.0202	0.0958	0.1596	0.2371	1.5852	64.1526	-25.0793
5	2.7565	-1.0087	1.7457	5.8196	-8.4935	19.9321	-0.1771	-0.1586	0.4021	0.447	0.146	-0.1126	-0.8081	-0.3925	0.0312	0.0508	-0.0208	-0.0162	0.0914	0.0172	0.1809	-8.9058	60.0335	-13.9398
6	0.6399	0.0288	1.2663	1.3067	-0.6189	2.8558	-0.564	-0.6284	0.2013	0.5677	0.6077	0.1774	-0.2037	-0.0298	-0.0436	0.1856	0.1576	0.0397	0.1036	0.0261	0.0684	5.1063	47.2749	-2.2824
7	1.0849	0.0837	-0.2797	2.4735	1.3893	2.6127	-0.0208	0.1096	-0.0605	0.0122	0.0072	0.0586	0.1612	-0.0752	0.0136	0.1305	0.0775	-0.0163	0.0434	-0.0084	0.0572	9.5091	35.9973	-14.0964
8	6.9083	-3.7727	-2.3641	2.6559	1.9077	6.4183	0.1805	0.2895	-0.018	-0.0232	-0.1333	-0.0314	-0.0275	-0.121	-0.0473	0.1093	0.067	-0.023	0.0398	-0.0221	0.1037	5.3556	38.2236	-17.565
9	5.2495	0.6108	-1.7424	2.5341	2.3799	6.8604	0.1538	0.0689	-0.3218	0.2812	-0.0315	0.1165	0.4546	0.0167	-0.1223	0.2736	0.0636	-0.0469	-0.0113	0.0111	0.062	8.6324	29.1405	-6.4687
10	4.5808	0.8053	1.2811	10.0696	-6.56	8.7551	-0.036	0.4326	-0.2399	-0.0009	0.2952	0.1015	1.0028	0.3046	-0.2592	0.2164	0.1549	-0.029	0.0486	-0.1203	0.0815	17.4269	25.7553	-15.5208
11	8.7774	5.7328	7.4828	13.7607	1.8735	7.2859	0.5368	0.9435	-0.7345	-0.578	0.1284	-1.2896	1.0685	1.3425	-0.6653	0.2076	0.2535	-0.0524	0.1669	-0.1357	0.0826	25.4743	30.4716	-13.7577
12	2.0422	-2.1743	0.5494	2.3481	-0.0724	8.0569	0.0491	-0.6532	-0.1287	0.3307	0.2095	0.2144	0.2301	-0.0356	-0.2586	0.2429	0.1083	-0.0303	0.0177	-0.0088	0.0398	13.3061	35.5351	-1.73
13	3.7019	0.7023	0.4529	2.6995	-0.725	2.0723	0.221	-0.0953	-0.3832	-0.2286	-0.1279	-0.2126	0.6597	0.0693	-0.0931	0.2803	-0.1424	-0.0235	0.0123	0.0174	0.0319	-14.6555	28.1139	-9.6638
14	4.7045	-0.4382	2.5908	6.0869	-3.6441	5.9493	0.1769	0.3978	-0.5341	-0.5847	-0.078	-0.2436	0.6684	0.2441	-0.0989	0.2509	-0.1051	0.0247	-0.0193	-0.0448	-0.0038	-14.7365	28.9941	-16.4101
15	2.8641	0.6691	-0.0208	3.9715	0.43	1.5213	-0.0797	0.2034	-0.2009	-0.2028	0.1499	-0.0676	0.4661	-0.2487	-0.0702	0.2416	-0.1487	-0.0152	0.0493	0.0314	-0.0195	-19.0906	31.856	-16.6498
16	1.8528	0.9899	1.1493	1.0853	0.4232	5.6375	0.1796	-0.1831	-0.2144	0.2703	-0.1113	-0.3374	0.1149	0.4006	-0.0683	0.0039	0.0079	-0.0901	0.1175	-0.0227	0.1119	52.4433	0.8534	-32.1513
17	5.8534	0.1685	0.9314	1.8174	0.557	1.9085	-0.0955	0.3508	0.3426	0.0978	0.0255	0.0632	-0.2201	0.0238	0.07	0.0661	-0.0026	-0.002	0.0635	-0.0326	0.0612	37.1052	6.7758	-48.1075
18	4.047	1.8699	-0.0328	1.3359	-0.1347	0.9316	-0.075	0.3192	0.2939	-0.0052	0.1017	0.1979	-0.1925	0.0188	-0.0267	0.0642	0.0258	-0.0161	0.1335	-0.0375	0.0875	33.0214	3.6119	-48.552
19	24.583	-4.5056	12.0112	0.8708	-0.9852	38.7719	1.1119	2.3468	0.1536	0.5569	-1.2191	1.9897	2.3318	-1.7602	0.1071	0.3085	0.0608	0.0286	0.2948	0.0637	0.3016	24.9475	8.8458	-60.9957
20	7.0657	0.0318	3.3052	6.2057	-3.8054	7.1224	-0.2932	0.9246	-0.0728	-0.5461	0.1322	-0.0577	0.1057	0.0335	0.161	0.0013	-0.0307	0.0249	0.2562	-0.114	0.0034	35.4563	-1.739	-60.3307
21	6.0875	-0.0634	-3.3501	0.0789	0.2748	2.5794	-0.4907	-0.1226	-0.4659	0.2448	0.1007	-0.1439	0.6876	0.1018	0.39	0.1039	0.0135	0.034	0.0562	-0.0438	0.1197	26.998	-7.8992	-38.629
22	4.9251	4.4562	0.8133	10.2075	1.4149	1.2134	-0.0265	-0.1783	0.0749	0.1808	0.0563	-0.2535	-0.005	0.0799	-0.0298	0.0767	0.0222	0.0053	0.0946	-0.089	0.0515	20.6675	9.756	-27.627
23	1.8413	-1.3737	-1.0097	4.9075	2.0347	2.5994	0.0642	0.0291	0.1068	-0.1703	-0.1768	-0.0384	-0.0122	-0.0173	0.1127	0.0457	0.009	0.0135	0.102	-0.0626	0.0888	21.8722	6.1526	-36.3558
24	3.3465	-0.7593	-1.2092	2.3582	-0.1162	1.717	0.1251	-0.3871	-0.0645	0.3773	-0.0638	-0.2548	0.0858	0.1735	-0.0613	0.1223	0.0006	-0.0389	0.1044	-0.0898	0.0118	23.8614	3.0313	-25.9502
25	3.6413	-4.1596	7.2883	12.5813	-14.2342	33.7539	0.2171	-0.3132	-0.0255	0.8985	0.2759	0.6409	-0.4386	-0.4752	-0.493	0.1259	-0.0226	0.0715	0.1323	-0.1606	0.0799	13.9725	11.8957	-22.1606
26	6.9965	-1.2846	0.9938	4.6017	-0.2682	4.5024	0.1949	-0.5243	0.4315	0.3515	-0.2291	0.3791	-0.0526	-0.3534	0.0341	0.0886	-0.0603	0.0783	0.1286	-0.1334	0.1022	9.9692	4.0506	-26.9678
27	1.8193	0.3769	-0.6811	1.3087	-0.2246	2.8797	0.1753	-0.5371	-0.1326	0.3622	-0.1845	-0.0595	-0.2591	-0.0883	0.0092	0.0965	-0.077	-0.0967	0.1534	-0.0664	0.0054	45.071	4.4051	-21.9006
28	10.9264	1.9101	9.0269	5.1574	-3.2449	16.7606	-0.1869	-0.3145	0.823	-0.0587	0.18	0.2147	-1.0855	-0.6365	0.0069	0.1514	-0.021	-0.056	0.0457	-0.0566	0.0503	48.4214	14.2134	-35.8911
29	7.3843	5.7698	-2.0965	5.4074	-2.6222	4.0189	0.0716	-0.6549	0.8165	0.2659	-0.1527	0.3923	-0.5783	-0.003	0.0811	0.1382	-0.0382	-0.0593	0.1194	-0.1643	0.0421	45.8351	13.8309	-23.479
30	1.9761	0.5008	0.7093	2.4835	1.5045	3.8847	0.0299	-0.2276	-0.0128	0.109	-0.1004	-0.1544	-0.2858	0.233	0.0705	0.0871	-0.0327	-0.0739	0.1125	-0.0505	0.0466	49.4798	7.5328	-31.8339
31	3.4457	-0.0238	-0.7383	3.6063	-0.8456	4.9785	0.1085	0.1055	0.7038	-0.0822	-0.1336	-0.3705	-0.7754	0.5293	0.0251	0.0657	-0.1401	0.0035	-0.067	0.0646	0.2745	84.5093	16.7591	-67.3473
32	5.4131	-0.2611	0.5717	1.7998	0.3086	0.7049	0.0783	0.1013	-0.0724	-0.1452	-0.0928	0.1465	-0.0695	-0.1849	0.0145	0.0634	-0.0224	0.0073	0.1153	-0.0355	0.0664	68.1819	-3.1546	-58.3782
33	4.9456	4.4589	0.6457	8.2999	-1.1643	3.8632	-0.0293	0.1791	-0.0714	-0.3755	0.0311	0.0863	0.1891	-0.2881	-0.0018	0.0597	-0.0264	0.0146	0.12	-0.0181	0.0691	70.1986	-6.4763	-63.3299
34	4.6804	0.5574	0.0693	2.2528	1.4153	1.2511	0.006	-0.0458	-0.1063	0.0433	-0.054	0.1655	0.167	-0.2395	0.048	0.0033	-0.0178	0.001	0.1409	-0.062	0.1058	59.4881	-2.2097	-54.527
35	2.0255	-4.388	-1.2488	12.2326	1.9057	22.0306	0.416	-0.2433	-0.9394	-0.1761	-0.3572	1.3806	0.1386	-2.4787	-0.0588	-0.0592	-0.1071	-0.0049	0.252	-0.0066	0.0759	56.8047	-13.8349	-50.9454
36	2.5004	0.3583	-0.326	21.2899	-1.0328	1.6397	0.1947	-0.5015	-0.0025	1.2925	-0.2055	-0.0381	0.1191	-0.0316	0.0107	0.0843	-0.0686	0.0199	0.1854	-0.0258	0.0435	68.5536	-8.0929	-46.1895
37	7.3126	-3.2925	-0.6224	6.8889	3.0998	4.8129	-0.2475	-1.1584	0.8092	0.1629	-0.0392	0.3858	-0.888	-0.6825	0.2867	0.0366	0.0212	0.0043	0.1179	-0.1734	0.091	61.7648	9.0986	-50.0649
38	4.4138	-0.4876	0.8138	4.3811	-2.3998	6.6552	0.0488	0.4996	0.6107	-0.1218	-0.0112	0.0398	0.2617	0.0408	-0.0375	-0.0373	0.045	-0.0322	0.0736	0.0975	0.1301	51.1224	13.169	-67.4021
39	6.0607	-0.979	3.3937	3.2118	-1.8146	8.6415	0.1669	0.425	0.2543	-0.4347	-0.0627	0.179	0.4075	-0.0946	-0.1042	0.0031	0.0473	-0.0123	0.0694	0.0044	0.0984	51.8496	7.6542	-68.0241
40	2.0651	1.8067	-2.2408	5.687	-1.4979	2.4835	0.3899	0.7804	0.4852	-0.2566	-0.1568	-0.1551	-0.3654	0.0413	-0.2331	0.0612	0.0952	0.0186	0.1381	0.1256	0.106	52.8796	18.1465	-69.3178
41	6.826	-4.9337	3.4842	3.867	-3.4886	4.9068	0.8176	1.1213	-0.2854	-2.2075	-0.1362	1.2272	-0.4145	-1.2231	-0.6814	0.4312	0.0235	-0.1852	0.4986	0.0813	0.4134	40.5127	13.3343	-78.0057
42	21.9979	7.2736	0.8564	7.9769	1.5059	3.9225	-0.0367	0.5175	1.8997	-0.0046	0.0972	0.6776	-0.565	-0.3243	-0.0605	0.0253	0.13	-0.0064	0.061	0.1359	0.0934	43.5887	17.8678	-64.8182
43	2.4979	-3.1466	-0.8354	13.534	-0.8352	2.0341	0.1669	0.6086	0.5922	-0.4775	-0.0544	0.4946	-0.5007	-0.1898	-0.1125	0.1078	-0.023	-0.0056	-0.0003	0.1595	0.1493	76.0624	17.0041	-73.3692
44	3.657	-0.9808	-0.7627	5.2604	-0.1236	2.5735	-0.0616	0.9068	0.4858	-0.4383	0.0059	0.0354	-0.231	-0.1499	0.0557	0.0521	-0.0573	0.01	0.1478	0.15	0.0322	76.6233	10.5406	-77.6649
45	4.851	-0.1425	0.8451	2.1772	0.5908	4.0848	-0.1262	0.454	0.442	-0.2617	-0.0462	-0.1377	-0.3775	0.1658	0.1724	0.0928	-0.0605	0.0075	0.0294	0.089	0.1268	79.2795	9.2597	-70.6571

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	206 - 244	7 - 45
2	X-RAY DIFFRACTION	2	A	A	245 - 288	46 - 89
3	X-RAY DIFFRACTION	3	A	A	289 - 308	90 - 109
4	X-RAY DIFFRACTION	4	A	A	309 - 322	110 - 123
5	X-RAY DIFFRACTION	5	A	A	323 - 335	124 - 136
6	X-RAY DIFFRACTION	6	A	A	336 - 346	137 - 147
7	X-RAY DIFFRACTION	7	A	A	347 - 383	148 - 184
8	X-RAY DIFFRACTION	8	A	A	384 - 390	185 - 191
9	X-RAY DIFFRACTION	9	A	A	391 - 404	192 - 205
10	X-RAY DIFFRACTION	10	A	A	405 - 416	206 - 217
11	X-RAY DIFFRACTION	11	A	A	417 - 430	218 - 231
12	X-RAY DIFFRACTION	12	A	A	431 - 443	232 - 244
13	X-RAY DIFFRACTION	13	A	A	444 - 460	245 - 261
14	X-RAY DIFFRACTION	14	A	A	461 - 478	262 - 279
15	X-RAY DIFFRACTION	15	A	A	479 - 520	280 - 321
16	X-RAY DIFFRACTION	16	C	C	206 - 243	7 - 44
17	X-RAY DIFFRACTION	17	C	C	244 - 274	45 - 75
18	X-RAY DIFFRACTION	18	C	C	275 - 305	76 - 106
19	X-RAY DIFFRACTION	19	C	C	306 - 313	107 - 114
20	X-RAY DIFFRACTION	20	C	C	314 - 332	115 - 133
21	X-RAY DIFFRACTION	21	C	C	333 - 347	134 - 148
22	X-RAY DIFFRACTION	22	C	C	348 - 365	149 - 166
23	X-RAY DIFFRACTION	23	C	C	366 - 387	167 - 188
24	X-RAY DIFFRACTION	24	C	C	388 - 403	189 - 204
25	X-RAY DIFFRACTION	25	C	C	404 - 415	205 - 216
26	X-RAY DIFFRACTION	26	C	C	416 - 443	217 - 244
27	X-RAY DIFFRACTION	27	C	C	444 - 458	245 - 259
28	X-RAY DIFFRACTION	28	C	C	459 - 468	260 - 269
29	X-RAY DIFFRACTION	29	C	C	469 - 490	270 - 291
30	X-RAY DIFFRACTION	30	C	C	491 - 520	292 - 321
31	X-RAY DIFFRACTION	31	E	E	206 - 235	7 - 36
32	X-RAY DIFFRACTION	32	E	E	236 - 266	37 - 67
33	X-RAY DIFFRACTION	33	E	E	267 - 284	68 - 85
34	X-RAY DIFFRACTION	34	E	E	285 - 308	86 - 109
35	X-RAY DIFFRACTION	35	E	E	309 - 319	110 - 120
36	X-RAY DIFFRACTION	36	E	E	320 - 332	121 - 133
37	X-RAY DIFFRACTION	37	E	E	333 - 341	134 - 142
38	X-RAY DIFFRACTION	38	E	E	342 - 359	143 - 160
39	X-RAY DIFFRACTION	39	E	E	360 - 388	161 - 189
40	X-RAY DIFFRACTION	40	E	E	389 - 404	190 - 205
41	X-RAY DIFFRACTION	41	E	E	405 - 424	206 - 225
42	X-RAY DIFFRACTION	42	E	E	425 - 444	226 - 245
43	X-RAY DIFFRACTION	43	E	E	445 - 460	246 - 261
44	X-RAY DIFFRACTION	44	E	E	461 - 489	262 - 290
45	X-RAY DIFFRACTION	45	E	E	490 - 520	291 - 321

-
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