PDB-2jk0: Structural and functional insights into Erwinia carotovora L- asp...

ID or keywords:

Entry

Database: PDB / ID: 2jk0

Title

Structural and functional insights into Erwinia carotovora L- asparaginase

Components

L-ASPARAGINASE

Keywords

HYDROLASE / ERWINIA / ENZYME THERAPY / PROTEIN STABILITY / LEUKEMIA TREATMENT

Function / homology

Function and homology information

asparagine metabolic process / asparaginase / asparaginase activity / cytosol
Similarity search - Function

Biological species

PECTOBACTERIUM CAROTOVORUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Papageorgiou, A.C. / Posypanova, G.A. / Andersson, C.S. / Sokolov, N.N. / Krasotkina, J.

Citation

Journal: FEBS J. / Year: 2008
Title: Structural and Functional Insights Into Erwinia Carotovora L-Asparaginase.
Authors: Papageorgiou, A.C. / Posypanova, G.A. / Andersson, C.S. / Sokolov, N.N. / Krasotkina, J.

History

Deposition	May 23, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jul 24, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2jk0.cif.gz	465.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2jk0.ent.gz	384.9 KB	Display	PDB format
PDBx/mmJSON format	2jk0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2jk0_validation.pdf.gz	502.4 KB	Display	wwPDB validaton report
Full document	2jk0_full_validation.pdf.gz	561.8 KB	Display
Data in XML	2jk0_validation.xml.gz	97.7 KB	Display
Data in CIF	2jk0_validation.cif.gz	132.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jk/2jk0 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/2jk0	HTTPS FTP

-
Related structure data

Related structure data	1hg1S 2vm7 PDB Unreleased entry S: Starting model for refinement
Similar structure data	2gvn-1 5i4b-1 5i3z-d 6pae-d 1o7j-d 1hfk-1 6uoh-1 1jsr-d 2hln-2 1jsl-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	#171 - Mar 2014 Neurotransmitter Transporters similarity (1)

Deposited unit

A: L-ASPARAGINASE

B: L-ASPARAGINASE

C: L-ASPARAGINASE

D: L-ASPARAGINASE

E: L-ASPARAGINASE

F: L-ASPARAGINASE

G: L-ASPARAGINASE

H: L-ASPARAGINASE

hetero molecules

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

1

A: L-ASPARAGINASE

B: L-ASPARAGINASE

C: L-ASPARAGINASE

D: L-ASPARAGINASE

hetero molecules

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

2

E: L-ASPARAGINASE

F: L-ASPARAGINASE

G: L-ASPARAGINASE

H: L-ASPARAGINASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.650, 135.630, 250.100
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	L-ASPARAGINASE Mass: 34328.074 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PECTOBACTERIUM CAROTOVORUM (bacteria) / Plasmid: ANSB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6Q4F4, asparaginase
#2: Chemical	ChemComp-ASP / ASPARTIC ACID Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₇NO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 45.82 % / Description: NONE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.81 Å / Relative weight: 1
Reflection	Resolution: 2.5→20 Å / Num. obs: 83599 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 14
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 78

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HG1

1hg1

Resolution: 2.5→20 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.91 / SU B: 23.414 / SU ML: 0.273 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.83 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.266	4197	5 %	RANDOM
R_work	0.188	-	-	-
obs	0.192	79398	96.1 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 34.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.13 Å²	0 Å²	0 Å²
2-	-	-1.57 Å²	0 Å²
3-	-	-	1.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18719	0	72	708	19499

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	19064
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.292	1.982	25885
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.952	5	2510
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.788	24.278	699
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.201	15	3202
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.211	15	112
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	3123
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14052
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	10760
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	13149
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	1233
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	0.183	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.291	0.2	6
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	0.333	1.5	12754
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.589	2	20194
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.975	3	6902
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.572	4.5	5691
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.57 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.344	252
R_work	0.252	4598

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	9.9429	11.1362	-7.2804	18.7761	-6.5667	9.675	0.5258	-0.3218	0.1501	0.8698	-0.1696	0.1538	-0.6606	-0.4336	-0.3562	0.2701	0.1483	-0.0188	0.0233	-0.0007	0.0218	-8.294	19.324	62.54
2	2.8106	-2.3546	4.077	6.1922	-0.9776	7.3227	0.2759	0.7122	0.5591	0.2928	-0.1975	0.8818	-0.9979	0.4137	-0.0784	0.2992	0.0229	-0.073	-0.0047	0.0073	0.2266	-10.536	23.628	55.003
3	0.6119	0.0926	0.0309	1.3861	-0.2016	0.8805	-0.0122	-0.1131	0.058	0.3216	-0.0621	0.0324	-0.2035	-0.1253	0.0743	0.3238	0.0146	-0.0104	0.0248	0.0142	0.0184	-1.712	10.808	60.797
4	1.2765	0.1498	-0.5213	1.7422	0.08	2.3682	-0.0431	-0.1863	0.145	0.3967	-0.0498	-0.2937	-0.2161	0.4303	0.0929	0.2095	-0.0587	-0.1651	0.0878	0.0639	0.0394	23.274	7.537	61.468
5	1.6823	0.1928	-0.1416	7.0757	-0.2899	3.0896	0.1073	0.1381	0.2053	0.0102	0.0276	0.6645	-0.3663	-0.4379	-0.1348	0.2313	0.2022	-0.1051	0.1535	0.0001	0.151	-18.493	15.673	28.809
6	0.6213	-0.0364	-0.4893	2.0408	1.2507	3.0443	0.0562	0.3476	0.0019	-0.2293	-0.1715	0.1903	-0.3593	-0.2619	0.1153	0.2319	0.1363	-0.1023	0.1427	0.0168	0.0412	-10.717	11.369	25.234
7	0.695	-0.0867	-0.1368	1.321	-0.491	0.7768	0.075	0.1834	-0.1107	-0.0034	-0.0694	0.0663	-0.0776	-0.0249	-0.0055	0.1623	0.0785	-0.073	0.0313	-0.0341	0.0211	-7.099	-3.763	28.304
8	0.7824	0.3877	-0.6766	2.1675	-0.7124	3.393	-0.1666	0.0485	-0.3042	-0.2648	0.1438	0.1897	0.0713	-0.0948	0.0229	0.1752	0.0493	-0.0866	-0.0222	-0.0503	0.0569	-5.801	-15.335	21.946
9	7.0572	0.9175	-0.0717	1.0344	2.6143	7.5229	-0.0147	0.1399	-0.4716	0.0501	-0.0492	-0.5007	0.8833	0.7559	0.064	0.2489	0.178	0.0104	0.1502	0.0939	0.1694	30.131	-12.793	30.459
10	1.0641	0.0049	-0.4938	1.3836	-0.1186	1.3302	0.0625	0.1339	-0.0859	-0.1541	-0.0963	-0.1931	0.0436	0.3409	0.0337	0.1513	0.0681	-0.0018	0.1736	0.0541	0.0687	22.48	-1.26	30.817
11	1.5273	0.4332	-0.7728	0.2735	-0.2751	2.3983	0.1283	0.2588	0.2269	0.0238	0.0418	-0.5186	0.174	0.2743	-0.1701	0.2639	-0.1215	-0.0317	0.0925	0.0967	0.1504	27.256	19.331	43.742
12	1.2003	0.0132	0.5019	2.1086	0.5284	2.728	0.0347	0.0684	0.3123	0.0722	-0.0578	-0.219	-0.3421	0.3206	0.0231	0.2085	-0.0563	-0.0313	0.0363	0.0794	0.0443	19.094	22.291	40.902
13	3.7269	1.2019	0.5668	3.5061	-1.4237	3.6066	0.1818	0.0076	-0.4433	-0.1285	-0.0882	-0.2949	0.793	0.5875	-0.0935	0.3217	0.1799	0.0314	0.0537	0.0019	0.2712	13.676	-29.713	48.353
14	1.2813	-0.3006	0.6756	1.346	-0.4389	0.8004	0.0827	0.0137	-0.2664	0.0871	-0.1027	0.0537	0.2466	-0.0204	0.02	0.2944	0.0454	-0.0395	-0.0267	0.0098	0.1593	2.698	-25.612	50.436
15	1.6177	0.2778	-0.3911	0.8904	-0.4354	1.8338	0.0089	0.0644	-0.1844	0.2636	-0.0439	-0.0049	0.1802	0.0576	0.0351	0.2545	0.0467	-0.0314	-0.0247	0.0401	0.0715	2.899	-13.337	53.882
16	1.5816	0.2116	1.1519	0.9836	-0.6795	2.761	0.0952	0.0801	-0.2772	0.1295	-0.0996	0.3182	0.1512	-0.2222	0.0044	0.1059	0.0124	0.0019	-0.0079	-0.062	0.1892	-20.267	-14.593	43.779
17	3.9269	-1.0053	1.58	1.5876	-1.0143	3.3609	0.1825	0.294	0.1455	-0.179	-0.2241	-0.1681	-0.7282	0.7815	0.0416	0.2812	-0.1577	0.0036	0.2343	0.0617	-0.1194	5.504	21.34	-45.484
18	0.1392	0.2297	0.4353	1.0117	-0.3894	3.3001	0.0494	0.288	-0.0218	-0.0484	-0.1184	-0.0847	-0.0089	0.3485	0.0689	0.163	-0.0362	-0.0587	0.2083	-0.0366	-0.0568	2.167	9.725	-37.738
19	6.7668	-0.604	-2.6918	0.1179	-0.3003	5.6357	0.0508	0.5855	0.0533	-0.0787	-0.1692	0.2032	-0.3958	-0.3939	0.1184	0.2072	-0.0168	-0.1119	0.0356	-0.0786	0.0287	-19.49	13.3	-43.35
20	1.2288	-0.5917	0.3277	1.0658	0.1211	2.9134	0.125	0.1112	0.1225	-0.1951	-0.0794	0.1649	-0.1016	-0.211	-0.0456	0.1769	0.0218	-0.1196	0.1333	-0.0515	0.0173	-24.014	7.256	-41.681
21	5.774	-2.317	-0.8903	6.7443	-0.3773	4.4671	0.1652	-0.3393	0.2508	0.5158	-0.188	-0.3364	-1.2029	0.7303	0.0229	0.3158	-0.4627	-0.1724	0.3456	-0.0103	-0.0556	15.33	18.386	-7.258
22	10.9725	-1.2667	6.9259	1.7189	-2.2493	5.7081	1.7805	0.9971	1.043	-0.7859	-0.4715	-2.3935	-0.7944	3.1019	-1.309	0.7122	-0.1545	-0.1453	0.6885	-0.0283	0.4808	19.61	21.572	-15.926
23	3.4112	-0.1243	-0.7651	1.8197	0.1781	1.3751	0.1914	-0.7222	0.1028	0.2743	-0.1889	-0.3085	-0.5253	0.6355	-0.0025	0.2915	-0.3667	-0.2125	0.5416	0.0856	-0.1376	16.27	11.041	-2.735
24	1.1967	-0.0021	0.1384	1.885	-0.7421	1.6298	0.0572	-0.334	-0.2669	0.287	-0.2022	-0.1228	-0.197	0.3103	0.1451	0.0814	-0.1089	-0.0896	0.2435	0.0832	-0.0073	6.666	-2.734	-6.637
25	1.6512	-0.7513	-0.2993	4.1849	-0.6933	1.7144	-0.1351	-0.1754	-0.0869	0.4951	0.2206	0.4588	-0.0189	-0.4437	-0.0855	0.0488	-0.0548	-0.0091	0.3201	0.0484	-0.0531	-32.65	-4.147	-9.205
26	0.4145	0.3599	-0.0523	1.5432	-0.9794	1.7545	0.0516	-0.1285	-0.1233	0.1422	-0.0077	0.1859	-0.2122	-0.2559	-0.0439	0.1293	-0.0063	-0.0218	0.1489	-0.032	-0.0092	-21.211	4.55	-15.059
27	4.854	-3.0625	0.3053	2.4796	-1.5837	3.5545	0.0229	-0.2323	0.2094	-0.0252	0.0311	0.4781	-0.6132	0.2034	-0.054	0.3533	-0.028	-0.0478	0.0037	-0.0608	-0.0044	-17.515	25.19	-26.435
28	4.191	-2.5593	2.2907	8.4648	-1.2729	2.3716	0.0128	-0.3563	0.2636	0.4223	-0.0446	0.1256	-0.4927	-0.1444	0.0318	0.3319	0.0448	0.0219	0.0644	-0.05	-0.0932	-20.776	21.748	-15.012
29	4.5034	-0.6416	0.5767	6.9169	-2.0265	1.3651	0.4094	-0.1584	-0.8416	-0.0352	-0.1606	0.3056	0.6353	-0.2825	-0.2488	0.0895	-0.0885	-0.0862	-0.05	-0.091	0.2896	-11.869	-29.292	-30.851
30	1.4649	-0.2992	0.3953	1.2521	-0.0195	0.7315	0.1059	0.1044	-0.2242	-0.2403	-0.0788	-0.0489	0.2121	0.024	-0.0271	0.2181	-0.0291	-0.0647	0.0633	-0.0566	0.1033	-3.927	-18.04	-32.403
31	2.2173	-0.2187	0.1228	1.5878	0.3174	1.5896	0.0971	0.1034	-0.4574	-0.1131	-0.241	-0.2506	0.0792	0.5985	0.1439	0.0527	0.0231	-0.0638	0.3537	0.1118	0.2462	19.866	-13.917	-22.975
32	7.4417	-2.4855	1.1381	0.9517	0.383	4.9662	0.1979	0.18	-0.3234	-0.2191	-0.342	-0.1963	0.5009	0.7039	0.144	0.1668	0.1106	0.0016	0.4021	-0.0417	0.1148	17.919	-13.55	-32.027

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 20
2	X-RAY DIFFRACTION	2	A	21 - 50
3	X-RAY DIFFRACTION	3	A	51 - 205
4	X-RAY DIFFRACTION	4	A	206 - 327
5	X-RAY DIFFRACTION	5	B	3 - 70
6	X-RAY DIFFRACTION	6	B	71 - 153
7	X-RAY DIFFRACTION	7	B	154 - 256
8	X-RAY DIFFRACTION	8	B	257 - 327
9	X-RAY DIFFRACTION	9	C	3 - 50
10	X-RAY DIFFRACTION	10	C	51 - 205
11	X-RAY DIFFRACTION	11	C	206 - 240
12	X-RAY DIFFRACTION	12	C	241 - 327
13	X-RAY DIFFRACTION	13	D	3 - 55
14	X-RAY DIFFRACTION	14	D	56 - 143
15	X-RAY DIFFRACTION	15	D	144 - 211
16	X-RAY DIFFRACTION	16	D	212 - 327
17	X-RAY DIFFRACTION	17	E	3 - 91
18	X-RAY DIFFRACTION	18	E	92 - 202
19	X-RAY DIFFRACTION	19	E	203 - 234
20	X-RAY DIFFRACTION	20	E	235 - 327
21	X-RAY DIFFRACTION	21	F	3 - 19
22	X-RAY DIFFRACTION	22	F	20 - 47
23	X-RAY DIFFRACTION	23	F	48 - 100
24	X-RAY DIFFRACTION	24	F	101 - 327
25	X-RAY DIFFRACTION	25	G	3 - 87
26	X-RAY DIFFRACTION	26	G	88 - 242
27	X-RAY DIFFRACTION	27	G	243 - 289
28	X-RAY DIFFRACTION	28	G	290 - 327
29	X-RAY DIFFRACTION	29	H	3 - 62
30	X-RAY DIFFRACTION	30	H	63 - 201
31	X-RAY DIFFRACTION	31	H	202 - 289
32	X-RAY DIFFRACTION	32	H	290 - 327

-
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

-
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