PDB-2wlf: Crystallographic analysis of the polysialic acid O-acetyltransfer...

ID or keywords:

Entry

Database: PDB / ID: 2wlf

Title

Crystallographic analysis of the polysialic acid O-acetyltransferase OatWY

Components

POLYSIALIC ACID O-ACETYLTRANSFERASE

Keywords

TRANSFERASE / ENZYME / ACETYLTRANSFERASE / LEFT-HANDED BETA HELIX

Function / homology

Function and homology information

polysialic-acid O-acetyltransferase activity / protein homotrimerization / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytosol
Similarity search - Function

Biological species

NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Lee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.

Citation

Journal: J.Biol.Chem. / Year: 2009
Title: Structural and Kinetic Characterizations of the Polysialic Acid O-Acetyltransferase Oatwy from Neisseria Meningitidis.
Authors: Lee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.

History

Deposition	Jun 23, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 30, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	2wlf.cif.gz	145.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2wlf.ent.gz	115.8 KB	Display	PDB format
PDBx/mmJSON format	2wlf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2wlf_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	2wlf_full_validation.pdf.gz	1.1 MB	Display
Data in XML	2wlf_validation.xml.gz	33.3 KB	Display
Data in CIF	2wlf_validation.cif.gz	43.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/2wlf ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wlf	HTTPS FTP

-
Related structure data

Related structure data	2wlcC 2wldC 2wleC 2wlgC C: citing same article (ref.)
Similar structure data	2wlg-d 2wld-d 2wle-d 2cw5-d 1ab8-2 2wlc-1 1wu8-d 2q6l-1 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	#165 - Sep 2013 Designed Protein Cages similarity (3) #39 - Mar 2003 lac Repressor similarity (3) #49 - Jan 2004 Carbonic Anhydrase similarity (3)

Deposited unit

A: POLYSIALIC ACID O-ACETYLTRANSFERASE

B: POLYSIALIC ACID O-ACETYLTRANSFERASE

C: POLYSIALIC ACID O-ACETYLTRANSFERASE

hetero molecules

74.2 kDa, 3 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)	78.855, 94.656, 100.829
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	16
Space group name H-M	P222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 6 - 214 / Label seq-ID: 6 - 214

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C

#1: Protein	POLYSIALIC ACID O-ACETYLTRANSFERASE Mass: 23731.191 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LEFT-HANDED BETA HELIX Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria) Strain: 406Y / Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: Q93S40
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN C, ASN 67 TO ILE

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 54 % Description: STARTING MODEL WAS MY NAI SOAKING SIRAS STRUCTURE SOLVED BY SHELX-CDE.
Crystal grow	pH: 4.6 Details: 100 MM SODIUM ACETATE, 2.25 M AMMONIUM ACETATE, pH 4.6

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979
Detector	Type: MBC NOIR-1 / Detector: CCD / Date: Jun 26, 2008 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.35→40 Å / Num. obs: 32150 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / R_merge(I) obs: 0.1 / Net I/σ(I): 15
Reflection shell	Resolution: 2.35→2.48 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0066	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 2.35→40 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.915 / SU B: 15.141 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23094	1631	5.1 %	RANDOM
R_work	0.18255	-	-	-
obs	0.18504	30518	99.96 %	-

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: 12.783 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.37 Å²	0 Å²	0 Å²
2-	-	-1.02 Å²	0 Å²
3-	-	-	-1.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4872	0	193	252	5317

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	5177
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4624
X-RAY DIFFRACTION	r_angle_refined_deg	1.468	1.979	7032
X-RAY DIFFRACTION	r_angle_other_deg	0.542	3.003	10713
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.8	5	649
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.147	25.735	211
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.785	15	899
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.393	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.157	0.2	822
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5635
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	903
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	0.397	1.5	3166
X-RAY DIFFRACTION	r_mcbond_other	0.072	1.5	1319
X-RAY DIFFRACTION	r_mcangle_it	0.769	2	5152
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.199	3	2011
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.058	4.5	1870
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

Refine LS restraints NCS

Ens-ID: 1 / Number: 3021 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	loose positional	0.6	5
2	B	loose positional	0.56	5
3	C	loose positional	0.54	5
1	A	loose thermal	2.52	10
2	B	loose thermal	2.4	10
3	C	loose thermal	2.1	10

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	125	-
R_work	0.226	2231	-
obs	-	-	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	7.0135	6.7817	3.6155	10.4235	6.646	8.0701	-0.1581	0.715	0.4865	-0.6437	0.3765	0.8743	-0.3732	-0.8682	-0.2184	0.3853	0.1532	-0.0592	0.499	0.2175	0.3377	22.2644	6.3126	-32.0933
2	0.4335	-0.3048	-0.4877	1.8948	0.6147	4.7651	-0.0024	0.0671	0.0296	-0.1026	0.027	0.1577	-0.065	-0.3437	-0.0246	0.1323	0.028	-0.0175	0.1661	0.036	0.1437	27.6666	0.681	-36.0654
3	1.9872	1.3452	1.5277	4.4693	-0.3117	2.3094	-0.1037	-0.0046	0.12	-0.0094	0.0239	0.308	0.2263	-0.4253	0.0798	0.2568	-0.141	0.0061	0.3341	-0.029	0.2204	27.2858	-6.6017	-36.3922
4	0.8076	-0.3887	-0.5801	3.4258	1.1046	3.8537	0.0056	0.0337	0.0124	-0.0309	0.0348	-0.0122	0.0649	0.0664	-0.0404	0.0735	-0.0207	-0.0183	0.16	0.0058	0.1223	32.3375	-8.1372	-31.7137
5	0.2764	-0.3702	-0.5275	1.2334	0.7398	2.2344	-0.0083	-0.028	-0.037	-0.0322	-0.033	-0.0086	0.2325	0.0738	0.0412	0.0839	-0.027	0.0198	0.1343	0.0217	0.1049	35.6379	-16.0931	-21.137
6	11.5502	-2.2563	-5.1656	5.2941	2.4766	9.2614	-0.3041	-0.6746	-0.3842	0.1928	0.1868	-0.4382	0.5683	0.793	0.1174	0.2081	0.0461	-0.0043	0.1841	0.04	0.1714	43.8812	-22.8162	-19.3336
7	4.9025	-0.3087	-1.6097	2.6551	-0.1802	3.8823	-0.0521	-0.0985	-0.2744	0.1602	0.0055	-0.1056	0.4775	0.2663	0.0466	0.2208	0.0383	0.0777	0.0832	0.0303	0.1755	43.5196	-29.289	-30.4123
8	10.6408	-4.1477	-1.4591	4.7046	-3.1541	6.0119	-0.0665	1.1317	0.4374	-0.1292	-0.0497	-0.3111	0.1114	-0.083	0.1162	0.2883	-0.0128	0.1644	0.494	0.1161	0.2696	49.5448	-26.7343	-44.0169
9	11.368	-3.1168	-2.0126	13.2106	6.9378	12.5738	-0.3838	0.6034	0.1043	0.248	0.3063	0.5122	1.0258	-0.6674	0.0775	0.5313	-0.1385	-0.0647	0.5082	0.0987	0.348	12.3561	-30.5697	-53.0532
10	5.9529	0.7511	-1.842	2.0837	-1.1316	4.6719	0.0885	0.1557	-0.1047	-0.2284	0.0024	0.2764	0.7277	-0.7612	-0.0909	0.4075	-0.2016	-0.0397	0.2608	-0.0206	0.1644	10.905	-38.2369	-47.9721
11	4.1866	-0.1346	-2.1462	0.4087	-0.4017	4.1986	0.1798	0.0575	-0.0244	-0.3171	-0.0274	-0.0004	0.5347	-0.3251	-0.1525	0.402	-0.1626	0.0189	0.2204	-0.0211	0.1776	15.854	-38.0693	-43.9239
12	8.0652	-0.0637	-3.2314	5.2985	0.2544	8.0884	0.129	0.2487	-0.1765	-0.2395	-0.0324	0.0412	0.2683	-0.3031	-0.0966	0.3427	-0.1583	-0.0172	0.1521	-0.0257	0.1063	19.3515	-37.1529	-40.9301
13	4.0344	-0.1095	-1.3226	1.1046	-0.9521	3.953	0.0948	0.0257	-0.1725	-0.1912	-0.0202	-0.0824	0.289	-0.2342	-0.0746	0.3732	-0.1629	0.0407	0.1491	-0.0288	0.166	19.758	-40.036	-34.1775
14	3.0781	1.56	-2.0196	1.0215	-1.1473	2.4705	-0.0682	-0.0225	-0.2433	-0.1787	0.0116	-0.1843	0.4061	0.0515	0.0566	0.3877	-0.0553	0.037	0.1173	-0.018	0.1998	32.6037	-38.9668	-33.154
15	2.1184	2.21	-1.0062	3.6377	-0.4269	2.3209	-0.033	-0.118	-0.3956	-0.1157	-0.0308	-0.3519	0.5278	0.1951	0.0639	0.4063	-0.0963	0.0163	0.1202	0.021	0.2033	25.1425	-45.8346	-20.0457
16	2.1302	2.7927	-1.2745	3.855	-1.4962	1.7666	-0.3633	0.3282	0.4958	-0.6976	0.4701	1.0097	0.307	-0.6699	-0.1068	0.6885	-0.3198	-0.2506	0.3716	0.104	0.9291	8.4732	-54.6081	-18.5859
17	21.5128	2.1522	-12.2504	11.0369	-15.8081	26.6929	0.2076	1.0365	0.3971	0.2158	-1.0628	-0.5711	-0.352	0.8364	0.8552	0.2468	-0.2695	-0.1488	0.7609	-0.2963	1.2083	-9.3803	-23.657	-15.3334
18	0.0963	0.6492	0.4751	4.9971	4.1039	3.6872	0.0628	-0.0209	0.192	0.2689	-0.3628	0.837	0.0115	-0.43	0.3	0.252	-0.0495	0.2272	0.4379	0.065	0.7351	-3.7483	-15.9501	-10.425
19	5.7943	4.4231	1.4654	9.576	2.1522	3.4056	0.0833	0.0186	0.3412	0.4671	-0.2444	0.4535	0.2362	-0.3131	0.1611	0.1311	-0.0704	0.0897	0.2741	-0.046	0.3278	-1.4522	-19.9551	-9.8917
20	12.4837	1.111	-1.0972	11.3195	-1.7831	7.9193	-0.2296	0.4166	-0.6064	-0.7657	0.0838	-0.0167	0.8514	-0.2726	0.1458	0.1684	-0.0809	0.0273	0.296	0.0277	0.208	4.029	-20.9201	-18.3526
21	2.5606	0.8001	0.2917	2.6321	0.1836	1.3919	-0.0911	-0.0036	0.0684	0.086	0.0609	0.2858	0.3074	-0.2688	0.0303	0.14	-0.1205	0.0546	0.2072	0.0223	0.1047	8.6386	-24.3334	-9.3133
22	4.4322	1.9994	-2.4396	11.6277	3.0592	4.7899	-0.0555	-0.1971	-0.3433	0.4209	0.0672	-0.1301	0.4566	0.0504	-0.0117	0.3595	-0.1735	0.0552	0.2701	-0.0198	0.1802	13.6982	-48.4771	-14.608
23	1.1168	1.0211	0.3715	2.1986	1.1798	0.7902	0.0314	-0.0183	-0.0917	0.2115	-0.0608	-0.004	0.2645	-0.1642	0.0295	0.2547	-0.1094	0.0479	0.1964	0.0334	0.1286	19.4734	-30.2081	-7.6737
24	1.6813	1.5068	0.3482	3.2937	0.5859	2.0856	0.0704	-0.1385	-0.0965	0.4396	-0.0747	-0.0094	0.2199	-0.1637	0.0043	0.1241	-0.0228	0.0429	0.1659	0.0168	0.0798	27.71	-17.9696	-1.8122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 11
2	X-RAY DIFFRACTION	2	A	12 - 38
3	X-RAY DIFFRACTION	3	A	39 - 53
4	X-RAY DIFFRACTION	4	A	54 - 93
5	X-RAY DIFFRACTION	5	A	94 - 169
6	X-RAY DIFFRACTION	6	A	170 - 176
7	X-RAY DIFFRACTION	7	A	177 - 200
8	X-RAY DIFFRACTION	8	A	201 - 214
9	X-RAY DIFFRACTION	9	B	5 - 9
10	X-RAY DIFFRACTION	10	B	10 - 44
11	X-RAY DIFFRACTION	11	B	45 - 65
12	X-RAY DIFFRACTION	12	B	66 - 81
13	X-RAY DIFFRACTION	13	B	82 - 116
14	X-RAY DIFFRACTION	14	B	117 - 159
15	X-RAY DIFFRACTION	15	B	160 - 197
16	X-RAY DIFFRACTION	16	B	198 - 214
17	X-RAY DIFFRACTION	17	C	6 - 10
18	X-RAY DIFFRACTION	18	C	11 - 26
19	X-RAY DIFFRACTION	19	C	27 - 45
20	X-RAY DIFFRACTION	20	C	46 - 51
21	X-RAY DIFFRACTION	21	C	52 - 118
22	X-RAY DIFFRACTION	22	C	119 - 127
23	X-RAY DIFFRACTION	23	C	128 - 168
24	X-RAY DIFFRACTION	24	C	169 - 214

-
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