PDB-3guc: Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP

ID or keywords:

Entry

Database: PDB / ID: 3guc

Title

Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP

Components

Ubiquitin-like modifier-activating enzyme 5

Keywords

TRANSFERASE /

ROSSMANN FOLD / ATP-BINDING / UBL CONJUGATION PATHWAY /

Structural Genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization / response to endoplasmic reticulum stress /

erythrocyte differentiation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Walker, J.R. / Bacik, J.P. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP
Authors: Walker, J.R. / Bacik, J.P. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.

History

Deposition	Mar 29, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Sep 6, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3guc.cif.gz	172.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3guc.ent.gz	133.6 KB	Display	PDB format
PDBx/mmJSON format	3guc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/3guc ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3guc	HTTPS FTP

-
Related structure data

Related structure data	1zfnS S: Starting model for refinement
Similar structure data	1t8p-d 4i5b-2 3wfp-7 4czx-d 4mb0-2 1ung-2 2x0j-1 3v3k-1 1pum-d 1uxi-d 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	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (3) #60 - Dec 2004 Ubiquitin similarity (4) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#203 - Nov 2016
Aminopeptidase 1 and Autophagy
similarity (3)
#60 - Dec 2004
Ubiquitin
similarity (4)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Ubiquitin-like modifier-activating enzyme 5

B: Ubiquitin-like modifier-activating enzyme 5

hetero molecules

65 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	77.394, 77.394, 205.892
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Ubiquitin-like modifier-activating enzyme 5 / Ubiquitin-activating enzyme 5 / Ubiquitin-activating enzyme E1 domain-containing protein 1 / UFM1- ...Ubiquitin-activating enzyme 5 / Ubiquitin-activating enzyme E1 domain-containing protein 1 / UFM1-activating enzyme / ThiFP1 Mass: 32165.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Plasmid: PET28A-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q9GZZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.51 Å³/Da / Density % sol: 51.05 %
Crystal grow	Temperature: 287 K / pH: 6.2 Details: 1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE,0.1 M SODIUM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2009
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 2.25→50 Å / Num. obs: 34922 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / R_sym value: 0.131 / Net I/σ(I): 23.878
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2.89 / R_sym value: 0.838 / % possible all: 100

-
Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHASER		phasing
REFMAC	5.5.0063	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ZFN

1zfn

Resolution: 2.25→40.82 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.9 / SU B: 10.761 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25485	1770	5.1 %	RANDOM
R_work	0.20303	-	-	-
obs	0.20562	33065	99.97 %	-
all	-	34835	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 55.853 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.96 Å²	0.48 Å²	0 Å²
2-	-	0.96 Å²	0 Å²
3-	-	-	-1.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→40.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3525	0	29	128	3682

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3624
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.531	1.962	4907
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.594	5	458
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.302	25.38	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.224	15	590
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.116	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	567
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2713
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.157	2	2297
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.967	3	3697
X-RAY DIFFRACTION	r_scbond_it	3.262	4	1327
X-RAY DIFFRACTION	r_scangle_it	4.252	5	1210
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.34	128	-
R_work	0.248	2392	-
obs	-	-	99.92 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	9.4028	-2.1937	2.1493	4.1628	1.5846	5.1727	0.0606	-0.945	-0.4068	0.4514	-0.0329	0.5246	0.1163	-0.2544	-0.0277	0.2365	0.0243	-0.0012	0.1878	0.011	0.1902	-44.4526	2.4502	-4.6377
2	2.2155	-1.3552	-1.2855	1.6123	-0.6292	3.3104	0.0209	-0.0346	0.2381	0.0934	-0.0566	-0.2514	-0.1999	0.1912	0.0357	0.1808	0.0625	-0.0032	0.1873	-0.0443	0.124	-39.5091	16.9882	-11.5278
3	1.2067	-0.0286	-0.2937	3.1862	-0.6209	4.5106	0.0893	-0.0653	0.1605	0.2378	0.0296	-0.1656	0.071	0.1873	-0.1189	0.1575	0.0752	-0.0139	0.2159	-0.0294	0.1189	-37.4364	12.4353	-9.7183
4	6.3268	2.3062	4.0962	1.1325	2.5856	7.4142	-0.0594	-0.2491	0.2792	0.0338	0.0225	-0.0379	-0.2814	0.4648	0.0369	0.5299	-0.0009	-0.1025	0.3604	-0.0056	0.5199	-26.6642	24.3203	-16.4518
5	1.606	0.5658	-2.9713	9.9496	1.8137	6.3369	0.2192	-0.6061	-0.0944	0.3074	-0.1419	-0.8886	-0.3501	1.1499	-0.0773	0.3326	-0.0238	-0.0478	0.4513	0.0069	0.3878	-23.992	21.0181	-15.4136
6	3.5182	2.6777	-3.8624	7.5317	-3.4256	4.3195	-0.1043	-0.2983	-0.1004	0.0098	-0.0093	-0.7083	0.1687	0.375	0.1136	0.2071	0.068	-0.0595	0.3371	-0.0304	0.245	-28.0334	12.5096	-9.5697
7	0.632	-0.4981	-0.13	2.7809	-1.6784	3.8015	-0.0169	0.0468	0.0234	-0.065	-0.1429	-0.4263	0.0242	0.4084	0.1598	0.1792	0.0852	0.0045	0.1877	-0.0168	0.1169	-35.9116	13.4486	-23.2923
8	3.7753	-0.4259	-1.1034	7.8033	-3.5773	5.3577	-0.069	-0.1646	-0.2479	-0.1657	0.0805	0.0686	0.3607	-0.1763	-0.0115	0.2116	0.1093	-0.0115	0.1274	-0.0306	0.1179	-42.6381	5.4984	-22.3318
9	1.7128	-0.3508	0.9091	0.5602	-0.043	3.0064	-0.0663	0.094	0.1425	0.0437	0.0484	-0.3559	-0.2409	0.0752	0.0179	0.1849	0.0666	0.0104	0.1654	-0.0285	0.2411	-44.3255	19.7556	-18.6269
10	6.0652	1.7275	-0.1694	5.0748	-0.528	4.1583	0.2075	0.1501	0.0097	-0.3853	-0.2577	-0.0667	0.1178	0.0948	0.0502	0.1543	0.106	-0.0077	0.0993	-0.0384	0.0521	-49.2954	18.1092	-23.4638
11	0.7542	1.2352	0.278	5.3986	3.7019	4.8368	0.0094	0.0362	0.1438	-0.526	0.116	-0.1925	-0.5681	0.3788	-0.1255	0.1803	0.0346	-0.0132	0.2029	-0.0178	0.197	-44.5116	31.0452	-10.5459
12	1.4251	-0.3701	-0.064	1.9625	-1.099	1.6235	-0.035	-0.0289	0.0177	-0.0999	-0.0346	0.0847	-0.0502	-0.183	0.0696	0.1473	0.065	-0.0165	0.1806	-0.0052	0.1158	-54.7455	24.6664	-17.3571
13	4.4178	4.2946	4.7973	4.2531	4.6709	5.2443	-0.9926	-0.0645	1.027	-0.8858	-0.0491	0.7986	-1.1758	0.0299	1.0417	0.8684	-0.0232	-0.1155	0.5654	-0.0473	0.923	-41.0211	42.2828	-4.9768
14	8.6052	6.8807	0.0059	6.2608	1.5198	6.0475	0.1681	-0.1041	0.0238	-0.069	-0.0138	-0.3751	-0.3424	0.5728	-0.1543	0.2213	0.0464	0.0513	0.242	0.0001	0.3715	-39.1097	30.6643	-2.9506
15	1.2255	-0.8561	0.23	0.8574	0.5391	2.1961	-0.055	-0.0926	-0.0377	0.0186	0.011	0.0871	0.0561	-0.039	0.044	0.1499	0.0278	-0.0005	0.1828	-0.0203	0.1288	-51.4817	22.1495	-4.2418
16	2.2593	2.3851	5.6674	2.6322	5.9194	14.629	-0.0689	0.0201	0.1508	-0.0701	-0.022	0.1755	-0.1894	-0.0178	0.091	0.1891	0.0181	-0.0002	0.2102	0.0115	0.2329	-61.6152	24.9689	-13.8722
17	4.0365	-0.8143	-0.5949	7.5911	1.6548	1.9761	0.1472	0.4324	0.0566	-0.4811	-0.1491	-0.0818	0.0066	-0.09	0.0019	0.1866	0.0208	-0.0273	0.1989	-0.0038	0.1309	-59.9235	20.3884	-29.2275
18	5.1586	1.1532	-0.5757	4.2123	-0.6473	0.436	0.0817	0.4676	-0.884	0.1965	-0.099	1.0793	0.1524	-0.4751	0.0173	0.4346	-0.201	-0.0597	0.7371	-0.3086	0.6641	-66.2391	12.6501	-24.0769
19	6.0677	-0.0827	-4.4489	7.0508	0.1847	6.7697	0.1491	0.8133	0.6279	-0.8764	0.0508	-0.0263	-0.3371	0.1802	-0.1999	0.2957	0.007	0.0234	0.3316	0.0601	0.2741	-30.1517	41.7797	6.9204
20	3.3559	-0.2156	0.259	0.7464	-1.3948	2.6141	0.1411	0.1741	-0.3242	-0.1076	-0.0511	0.0538	0.2031	0.106	-0.0899	0.102	0.0418	-0.0224	0.2532	-0.0426	0.1331	-35.4499	25.3832	13.0396
21	5.8416	1.9271	1.2984	7.4337	0.7814	4.4906	-0.0936	0.4972	-0.1489	-0.5098	0.0241	0.0505	-0.0797	0.0047	0.0695	0.0628	0.0233	-0.0109	0.251	-0.0242	0.0798	-30.3912	30.3454	7.0356
22	8.6503	-0.7516	-4.7371	0.4183	0.0566	5.278	-0.2666	-0.114	-1.0287	0.0504	0.0397	0.0489	0.7828	0.0289	0.227	0.2133	-0.0114	-0.0553	0.2941	-0.0159	0.2298	-29.5187	21.022	19.8589
23	1.877	0.022	-1.187	1.0928	-0.0614	4.4312	-0.0473	-0.0301	-0.1656	0.0301	-0.0627	-0.1455	0.1175	0.345	0.11	0.0099	0.013	-0.0219	0.274	-0.02	0.1266	-28.1595	27.8648	20.4871
24	5.4669	1.6166	2.1413	3.4075	2.522	3.7999	0.1683	-0.1523	0.1096	0.0077	-0.2076	-0.3193	-0.1978	0.0994	0.0393	0.1691	0.0017	-0.0096	0.2732	0.0117	0.1724	-33.6229	34.8175	18.3681
25	2.2471	-1.4591	-0.9946	7.0877	0.311	4.0489	-0.008	-0.2778	-0.3083	-0.1247	0.0939	-0.0978	0.3356	-0.0646	-0.0859	0.1191	0.0156	-0.0269	0.2984	0.0091	0.1204	-43.8703	26.2466	25.6896
26	5.1453	-0.5253	-0.9367	3.2292	0.7062	0.3914	0.0105	-0.4731	0.1401	0.1815	-0.0472	-0.2262	0.0253	0.1215	0.0367	0.1745	-0.0278	-0.0355	0.2598	-0.0227	0.1441	-41.6486	36.7875	24.1238
27	2.196	3.3722	1.5994	6.3335	2.3888	5.096	0.31	-0.2712	-0.3022	0.0289	-0.4913	-0.1309	0.7334	-0.4112	0.1814	0.2985	-0.0083	-0.075	0.2613	-0.0001	0.2454	-47.2738	20.4365	12.9411
28	1.6057	1.1102	0.4728	8.9327	3.446	2.7825	0.0452	-0.0269	-0.0367	0.1333	-0.1018	0.0255	0.1191	-0.1172	0.0565	0.1333	0.0101	0.004	0.181	0.0134	0.1384	-49.0204	28.9194	13.5216
29	4.1087	1.2152	0.6887	0.7989	-0.749	2.5558	0.0735	-0.0401	-0.1252	-0.0951	-0.0746	0.0425	0.1373	-0.0203	0.0011	0.1484	0.0729	-0.0288	0.2375	-0.0249	0.1875	-54.3308	30.4132	19.8298
30	7.3697	-6.3972	0.6965	6.6866	-0.3108	0.1465	0.4405	0.101	-0.7551	-0.134	-0.2594	0.172	0.1423	-0.0665	-0.1811	0.5109	-0.12	-0.027	0.4472	-0.0397	0.3341	-48.3399	12.1826	4.5225
31	3.9832	2.6396	1.2714	8.8746	1.1461	3.1253	0.0736	0.0554	-0.1881	-0.2753	-0.0813	-0.1083	0.0926	0.0278	0.0077	0.0821	0.035	-0.001	0.1988	-0.0121	0.0948	-43.2499	25.3118	5.1092
32	5.5078	0.9189	3.7931	8.8849	1.3426	4.7576	-0.0077	0.1724	0.2781	-0.1714	-0.0794	-0.0178	-0.467	0.0274	0.0871	0.1289	-0.0088	0.002	0.2466	-0.0131	0.1166	-40.3576	39.3208	7.3272
33	1.5493	-0.9729	-0.0242	0.6141	0.0794	1.6983	0.0178	0.0237	0.0895	-0.0233	-0.0163	-0.0476	-0.1789	0.061	-0.0015	0.1384	0.0067	-0.0058	0.1944	-0.0247	0.1317	-50.1022	32.7608	7.3908
34	1.9582	0.3062	-0.5042	9.0065	4.1433	3.3473	-0.0106	0.0118	-0.1592	-0.1392	-0.0855	0.0794	0.0748	-0.1812	0.0961	0.1344	0.0284	-0.0206	0.2209	-0.0138	0.1452	-56.4464	24.5308	4.0898
35	3.8664	0.252	0.6364	4.2581	1.0851	2.2874	-0.0324	-0.5641	0.0315	0.4595	0.0678	-0.0015	-0.2052	-0.0815	-0.0354	0.1277	0.0386	0.0042	0.2822	-0.0283	0.1004	-53.123	37.2217	28.7626
36	5.467	0.4534	-2.1019	8.8309	0.7201	3.3924	0.0873	-0.4907	0.9953	-0.3024	-0.0491	-0.1806	-0.811	-0.2628	-0.0382	0.3909	0.0503	-0.0311	0.2931	-0.1417	0.2839	-49.8443	47.4772	26.9155

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	69 - 73
2	X-RAY DIFFRACTION	2	A	74 - 89
3	X-RAY DIFFRACTION	3	A	90 - 104
4	X-RAY DIFFRACTION	4	A	105 - 121
5	X-RAY DIFFRACTION	5	A	122 - 127
6	X-RAY DIFFRACTION	6	A	128 - 139
7	X-RAY DIFFRACTION	7	A	140 - 159
8	X-RAY DIFFRACTION	8	A	160 - 173
9	X-RAY DIFFRACTION	9	A	174 - 186
10	X-RAY DIFFRACTION	10	A	187 - 202
11	X-RAY DIFFRACTION	11	A	203 - 214
12	X-RAY DIFFRACTION	12	A	215 - 235
13	X-RAY DIFFRACTION	13	A	236 - 251
14	X-RAY DIFFRACTION	14	A	252 - 260
15	X-RAY DIFFRACTION	15	A	261 - 293
16	X-RAY DIFFRACTION	16	A	294 - 299
17	X-RAY DIFFRACTION	17	A	300 - 311
18	X-RAY DIFFRACTION	18	A	312 - 329
19	X-RAY DIFFRACTION	19	B	69 - 74
20	X-RAY DIFFRACTION	20	B	75 - 88
21	X-RAY DIFFRACTION	21	B	89 - 100
22	X-RAY DIFFRACTION	22	B	101 - 128
23	X-RAY DIFFRACTION	23	B	129 - 168
24	X-RAY DIFFRACTION	24	B	169 - 183
25	X-RAY DIFFRACTION	25	B	184 - 195
26	X-RAY DIFFRACTION	26	B	196 - 202
27	X-RAY DIFFRACTION	27	B	203 - 211
28	X-RAY DIFFRACTION	28	B	212 - 220
29	X-RAY DIFFRACTION	29	B	221 - 237
30	X-RAY DIFFRACTION	30	B	238 - 255
31	X-RAY DIFFRACTION	31	B	256 - 267
32	X-RAY DIFFRACTION	32	B	268 - 275
33	X-RAY DIFFRACTION	33	B	276 - 286
34	X-RAY DIFFRACTION	34	B	287 - 295
35	X-RAY DIFFRACTION	35	B	296 - 310
36	X-RAY DIFFRACTION	36	B	311 - 319

-
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