PDB-2w1k: Crystal Structure of Sortase C-3 (SRTC-3) from Streptococcus pneu...

ID or keywords:

Entry

Database: PDB / ID: 2w1k

Title

Crystal Structure of Sortase C-3 (SRTC-3) from Streptococcus pneumoniae

Components

PUTATIVE SORTASE

Keywords

TRANSFERASE / PILUS / SORTASE / PNEUMOCOCCUS / PATHOGENICITY

Function / homology

Function and homology information

membrane => GO:0016020 / hydrolase activity
Similarity search - Function

Biological species

STREPTOCOCCUS PNEUMONIAE (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.14 Å

Authors

Manzano, C. / Contreras-Martel, C. / El Mortaji, L. / Izore, T. / Fenel, D. / Vernet, T. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A.

Citation

Journal: Structure / Year: 2008
Title: Sortase-Mediated Pilus Fiber Biogenesis in Streptococcus Pneumoniae.
Authors: Manzano, C. / Contreras-Martel, C. / El Mortaji, L. / Izore, T. / Fenel, D. / Vernet, T. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A.

History

Deposition	Oct 17, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 23, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 23, 2018	Group: Data collection / Structure summary / Category: struct / Item: _struct.title
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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA" IN EACH CHAIN ON SHEET RECORDS ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2w1k.cif.gz	112.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2w1k.ent.gz	89.1 KB	Display	PDB format
PDBx/mmJSON format	2w1k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2w1k_validation.pdf.gz	450.5 KB	Display	wwPDB validaton report
Full document	2w1k_full_validation.pdf.gz	460.5 KB	Display
Data in XML	2w1k_validation.xml.gz	24.8 KB	Display
Data in CIF	2w1k_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w1/2w1k ftp://data.pdbj.org/pub/pdb/validation_reports/w1/2w1k	HTTPS FTP

-
Related structure data

Related structure data	2w1jSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ofk-1 1nf8-d 2ei9-d 1nf9-d 6sf7-1 6qmt-1 6qhc-2 6jjq-d 1uhb-d 4k8y-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: PUTATIVE SORTASE

B: PUTATIVE SORTASE

hetero molecules

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

1

A: PUTATIVE SORTASE

hetero molecules

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

2

B: PUTATIVE SORTASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	122.638, 122.638, 122.638
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	195
Space group name H-M	P23

#1: Protein	PUTATIVE SORTASE / SORTASE C-3 / SORTASE D Mass: 28412.365 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PLIM (PROTEIN EXPERT, GRENOBLE) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RIL CELLS (INVITROGEN) References: UniProt: Q97SB7, UniProt: A7KT36*PLUS, EC: 2.3.2.12
#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SIGNAL PEPTIDE AND TRANSMEMBRANE DOMAIN DELETED

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.96 % / Description: NONE
Crystal grow	pH: 5 / Details: 100 MM MES PH 5.0, 0.5 M (NH4)2SO4, 1.0 M LISO4

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU ROTAFLEX / Wavelength: 1.5418
Detector	Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 31, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.14→43.35 Å / Num. obs: 31007 / % possible obs: 90.8 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / B_iso Wilson estimate: 35.09 Å² / R_sym value: 0.1 / Net I/σ(I): 14.3
Reflection shell	Resolution: 2.14→2.27 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.2 / R_sym value: 0.52 / % possible all: 76.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.4.0067	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1J

2w1j

Resolution: 2.14→43.35 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.917 / SU B: 9.811 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.241	1674	5 %	RANDOM
R_work	0.18	-	-	-
obs	0.183	32021	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 37.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→43.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3296	0	24	505	3825

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.028	0.022	3422
X-RAY DIFFRACTION	r_bond_other_d	0.028	0.022	3422
X-RAY DIFFRACTION	r_angle_refined_deg	2.296	1.963	4658
X-RAY DIFFRACTION	r_angle_other_deg	2.296	1.963	4658
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.975	5	422
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.436	24.699	166
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.988	15	562
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.207	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.225	0.2	512
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	2638
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	1.457	1.5	2088
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.474	2	3388
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.837	3	1334
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.459	4.5	1266
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: 2.14→2.2 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.297	135
R_work	0.251	2294

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	13.5127	2.4571	-1.8797	7.9794	-0.7852	9.6521	-0.0578	-0.0792	-0.5973	0.0642	0.0377	0.716	0.2336	-0.7804	0.0202	0.1796	-0.0104	0.0168	0.1693	-0.0137	0.1229	38.5695	11.519	-14.5021
2	4.5285	-3.1247	3.1133	2.4195	-1.4911	3.7804	-0.0417	-0.1807	-0.7396	0.2049	0.1637	0.4399	0.555	-0.4665	-0.122	0.1827	-0.0033	0.0212	0.1813	0.0201	0.2175	47.273	9.4452	-8.9453
3	9.1758	-0.0808	-1.1622	6.5178	0.7672	10.819	-0.0435	-0.3707	-0.5486	0.3258	0.0513	0.1032	0.5697	-0.1583	-0.0078	0.0974	0.0095	-0.012	0.1188	-0.0039	0.122	55.2911	8.0078	-13.1469
4	3.0268	-1.8176	-0.9472	2.4566	1.2181	7.0306	-0.0253	0.1039	0.0617	-0.1352	-0.0901	-0.3118	-0.0635	0.2723	0.1155	0.0524	-0.0026	-0.0098	0.0595	-0.009	0.1326	60.6986	6.7903	-25.2511
5	18.2568	-8.8257	3.7808	4.8556	-1.2808	1.2907	0.4746	0.7676	-1.3812	-0.2163	-0.15	-0.0526	0.8934	0.7709	-0.3246	0.2731	-0.0137	0.0271	0.267	0.0313	0.2765	58.6426	5.171	-38.7609
6	21.791	-15.9436	-5.4903	12.0838	3.2443	2.8102	-0.0112	0.6954	-1.0024	-0.4097	-0.0485	0.4799	0.9792	-0.2111	0.0597	0.2186	-0.0024	-0.0078	0.2092	0.0106	0.203	45.2791	6.599	-40.2339
7	11.4795	-7.1919	-13.659	5.3938	8.281	16.3385	1.0344	1.8189	-2.8539	-2.6748	-0.0105	1.6548	-1.093	-1.6512	-1.0239	0.8344	-0.0796	-0.257	0.3368	-0.0027	0.5118	47.7453	-1.3109	-36.6705
8	8.4476	-1.6442	3.225	8.5385	-2.6785	1.743	0.1756	-0.0875	-0.3633	0.0021	0.0077	-0.0086	0.1817	0.1459	-0.1833	0.0586	0.0248	-0.0075	0.0641	-0.0058	0.0927	53.5307	0.2255	-23.599
9	1.2996	-0.7927	0.9034	2.1675	-0.9448	1.2939	-0.0566	-0.1039	0.017	0.142	0.0048	0.066	-0.0507	-0.2315	0.0518	0.0785	0.0116	-0.0047	0.1056	-0.0256	0.0695	41.2316	13.5581	-23.4133
10	11.5239	-0.461	0.8643	1.0922	-2.1338	6.8309	0.0763	0.6362	-0.6189	-0.2172	0.0514	0.2081	0.7557	-0.1027	-0.1277	0.1132	-0.0004	0.0037	0.0666	0.0149	0.1202	43.6067	3.3617	-30.042
11	1.357	-0.2203	-0.3468	2.4429	3.0371	3.7798	-0.0841	-0.0686	-0.1529	0.4254	-0.05	0.102	0.243	-0.3373	0.1341	0.0879	-0.0077	-0.026	0.0988	-0.0142	0.1092	39.5091	5.2577	-29.1048
12	2.6522	-0.0196	-0.1942	1.5721	-0.4284	1.0606	-0.015	0.0344	0.1036	0.0375	-0.0108	-0.027	-0.0446	0.0291	0.0258	0.0608	0.0034	-0.0037	0.0642	-0.0042	0.059	52.5064	13.2878	-30.2863
13	6.2572	3.981	-0.8485	6.5487	-3.5437	6.7197	0.1271	-0.3734	-0.5116	0.2259	0.1732	-0.0443	0.2453	-0.4586	-0.3003	0.1091	0.0348	-0.0465	0.1621	-0.0046	0.1641	31.5878	10.923	-34.2513
14	3.0021	3.194	-1.202	3.4737	-1.3264	0.5112	-0.0307	-0.3645	-0.0693	0.0413	0.0166	-0.0222	-0.313	-0.0884	0.0141	0.122	0.0475	-0.0646	0.1625	-0.0366	0.0791	34.4301	16.6496	-33.0002
15	2.0467	0.3361	0.1772	1.0167	0.9343	1.495	-0.0105	0.2036	0.2169	-0.1517	-0.0534	0.1922	-0.1993	-0.1306	0.064	0.0824	0.0347	-0.0207	0.1053	-0.0187	0.1394	41.4781	26.5411	-30.8518
16	5.0079	0.2556	1.3938	0.531	1.6268	5.0609	0.0236	-0.2393	-0.1097	0.1108	-0.0124	0.0459	0.1408	0.0442	-0.0112	0.0831	0.0018	0.0048	0.0778	-0.0176	0.0986	49.0898	16.8036	-16.3832
17	1.902	-0.7302	3.5661	0.9225	-1.4814	12.1599	-0.0233	0.2476	0.2703	-0.2368	-0.0349	0.0456	-0.4872	0.1902	0.0582	0.103	-0.0077	-0.0015	0.1043	-0.007	0.1423	48.9259	25.9971	-29.5328
18	1.4085	0.181	0.9346	0.3784	0.112	0.814	-0.0326	0.2263	-0.0548	-0.1763	-0.0021	-0.0691	-0.0241	0.13	0.0348	0.1026	-0.0003	-0.0152	0.1	0.0057	0.0817	49.6531	16.7864	-40.3165
19	1.2336	0.6317	1.3164	0.7729	0.6485	3.5431	-0.0571	0.0956	-0.0113	-0.143	0.1027	0.0262	-0.3635	-0.0547	-0.0456	0.0483	0.0386	-0.0183	0.0735	0.0011	0.0962	47.0761	20.3254	-31.4059
20	1.4063	-1.3537	2.2777	2.8372	0.6524	8.9651	0.1067	-0.108	0.0233	-0.0195	-0.1644	0.1248	-0.2837	-0.3315	0.0577	0.0757	0.0455	0.0231	0.0949	-0.0024	0.1045	43.2894	25.061	-12.1696
21	12.0336	-0.5228	1.9599	0.055	0.402	7.6727	0.0152	0.015	0.474	0.1378	-0.0909	-1.1466	-0.6812	1.3004	0.0757	0.2196	0.0222	-0.0043	0.1848	-0.0111	0.231	86.4231	14.931	-12.2432
22	3.5003	2.9285	-0.6075	11.4969	-4.2265	2.844	-0.2463	-0.8954	-0.9341	0.6864	0.1173	0.1577	0.5923	-0.0633	0.129	0.1741	0.0048	0.0014	0.2037	0.0104	0.1814	78.194	11.0563	-9.9087
23	5.9229	-2.3601	0.1121	11.0025	-0.3353	5.702	-0.0615	-0.4349	-0.3902	0.5011	0.0709	-0.2603	0.4706	0.3569	-0.0094	0.107	-0.017	0.0081	0.1537	-0.0035	0.1384	67.8193	12.166	-8.1635
24	3.2209	0.9884	-1.5823	8.2932	1.8695	4.7099	0.0508	0.0312	0.1354	-0.1997	-0.0148	0.3543	-0.2566	-0.3137	-0.036	0.0385	-0.001	0.0003	0.0907	-0.004	0.045	61.9459	25.2499	-6.7865
25	8.1342	0.7112	-4.801	0.0704	-0.229	7.2796	0.2034	-0.961	0.6631	0.5932	-0.2606	0.6721	-0.3702	-0.2535	0.0572	0.238	0.0299	0.0032	0.2495	0.0046	0.2843	64.1548	38.877	-5.2703
26	29.3914	-9.1395	-11.5303	5.0913	6.7113	9.0979	-0.0999	-1.5267	0.9271	0.8849	0.1257	-0.2571	-0.5493	0.3684	-0.0258	0.1975	-0.0083	0	0.1796	0.0248	0.1781	77.3761	40.3171	-6.5311
27	11.4747	-14.1922	-6.3783	17.5533	7.8888	3.5454	1.1984	-2.0162	2.2935	-0.9204	-1.4263	-0.7687	-1.9804	2.1798	0.2279	0.8302	-0.4011	-0.0878	0.6748	0.0905	0.4543	74.8142	36.7347	1.5206
28	7.5526	3.5033	-8.7497	1.625	-4.0586	10.1367	0.0348	-0.2857	0.1311	0.3634	0.0059	0.1315	-0.2533	0.5118	-0.0406	0.0544	0.0084	-0.0109	0.102	0.0027	0.0664	68.7363	24.5854	-0.8216
29	4.0163	-1.6719	0.7025	4.8508	0.1928	6.6759	-0.0816	-0.1777	-0.3246	0.2634	0.0654	-0.0288	0.2059	0.1084	0.0162	0.0492	-0.0185	-0.008	0.0575	0.004	0.0878	75.7603	20.9525	-2.8626
30	2.5383	0.1799	-2.7633	2.323	-1.3595	8.0556	-0.1045	0.0659	-0.0699	-0.0614	0.1	-0.3393	0.2538	0.0976	0.0045	0.0675	-0.0055	0.0215	0.0661	-0.042	0.1255	83.9133	24.3904	-18.2965
31	7.6162	-0.3084	-2.0775	8.6888	-1.8646	2.6982	0.0017	-0.4517	0.3841	0.5166	-0.0014	-0.3987	-0.2775	0.3357	-0.0002	0.1118	0.0032	0.0009	0.1198	0.0009	0.0833	80.131	29.6758	-2.9087
32	2.2153	0.4783	0.2145	1.859	0.4088	0.1808	-0.059	-0.0203	-0.0275	0.0365	0.0398	-0.0278	-0.0661	0.0716	0.0192	0.0807	-0.0105	0.0109	0.0901	0.0022	0.0405	74.0487	29.3587	-9.4996
33	4.3961	0.68	0.1071	0.7532	-0.1109	0.5156	0.0015	-0.0123	-0.103	-0.1158	0.0224	-0.0645	-0.076	-0.0734	-0.0239	0.0756	-0.0143	-0.0027	0.1024	-0.0077	0.0942	72.4701	31.8874	-15.7358
34	3.3588	0.8909	4.3698	2.7608	0.1881	12.6388	0.0173	-0.5016	-0.4219	0.6607	-0.078	-0.0859	0.5888	-0.0948	0.0607	0.1514	-0.0216	0.0164	0.175	0.0088	0.2149	92.035	32.6871	-10.281
35	5.7543	-4.9468	4.656	4.2526	-4.0026	3.7674	0.1367	-0.1873	-0.2184	-0.5217	-0.035	-0.0648	-0.1518	-0.0925	-0.1017	0.1079	-0.0941	0.0455	0.0852	-0.0803	0.1599	87.6556	33.2869	-16.8813
36	1.4914	0.9087	0.1004	0.7433	0.7135	2.2506	-0.0604	0.1246	0.1221	-0.1812	0.0148	-0.0757	-0.1268	0.2509	0.0455	0.0766	-0.0151	0.0296	0.1065	-0.0025	0.1251	80.4021	29.7462	-25.3031
37	7.602	2.8729	-1.575	7.9289	2.0499	1.3487	-0.0368	-0.0969	-0.2738	0.311	-0.092	-0.1501	0.111	0.0324	0.1289	0.0631	0.0015	0.0013	0.0844	-0.0172	0.0873	73.2818	14.9539	-16.8599
38	2.1941	3.1622	-1.0302	7.6794	-0.9389	1.1763	-0.0583	0.1343	0.049	-0.2684	0.0024	0.1035	-0.2048	0.1895	0.0559	0.0911	-0.0223	-0.0082	0.1227	-0.0202	0.0424	73.2946	28.4442	-25.9244
39	0.7624	0.636	0.1366	1.0636	0.0243	0.3578	-0.023	0	0.1587	-0.0699	0.0142	0.0611	-0.1365	0.0041	0.0088	0.0845	-0.015	0.0008	0.0827	0.0042	0.0824	74.0852	36.7174	-18.3525
40	0.7911	1.8811	-1.4309	8.5216	-0.1924	5.133	0.0069	0.1291	-0.18	-0.2486	0.1168	-0.3705	-0.0868	0.2944	-0.1237	0.0847	0.0272	0.032	0.0988	-0.0056	0.1083	79.3745	12.1378	-25.0518

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	37 - 43
2	X-RAY DIFFRACTION	2	A	44 - 49
3	X-RAY DIFFRACTION	3	A	50 - 56
4	X-RAY DIFFRACTION	4	A	57 - 67
5	X-RAY DIFFRACTION	5	A	68 - 72
6	X-RAY DIFFRACTION	6	A	73 - 77
7	X-RAY DIFFRACTION	7	A	78 - 83
8	X-RAY DIFFRACTION	8	A	84 - 89
9	X-RAY DIFFRACTION	9	A	90 - 109
10	X-RAY DIFFRACTION	10	A	110 - 115
11	X-RAY DIFFRACTION	11	A	116 - 122
12	X-RAY DIFFRACTION	12	A	123 - 144
13	X-RAY DIFFRACTION	13	A	145 - 150
14	X-RAY DIFFRACTION	14	A	151 - 155
15	X-RAY DIFFRACTION	15	A	156 - 166
16	X-RAY DIFFRACTION	16	A	167 - 173
17	X-RAY DIFFRACTION	17	A	174 - 181
18	X-RAY DIFFRACTION	18	A	182 - 210
19	X-RAY DIFFRACTION	19	A	211 - 228
20	X-RAY DIFFRACTION	20	A	229 - 242
21	X-RAY DIFFRACTION	21	B	36 - 42
22	X-RAY DIFFRACTION	22	B	43 - 47
23	X-RAY DIFFRACTION	23	B	48 - 56
24	X-RAY DIFFRACTION	24	B	57 - 67
25	X-RAY DIFFRACTION	25	B	68 - 72
26	X-RAY DIFFRACTION	26	B	73 - 77
27	X-RAY DIFFRACTION	27	B	78 - 83
28	X-RAY DIFFRACTION	28	B	84 - 88
29	X-RAY DIFFRACTION	29	B	89 - 96
30	X-RAY DIFFRACTION	30	B	97 - 109
31	X-RAY DIFFRACTION	31	B	110 - 117
32	X-RAY DIFFRACTION	32	B	118 - 132
33	X-RAY DIFFRACTION	33	B	133 - 145
34	X-RAY DIFFRACTION	34	B	146 - 151
35	X-RAY DIFFRACTION	35	B	152 - 155
36	X-RAY DIFFRACTION	36	B	156 - 167
37	X-RAY DIFFRACTION	37	B	168 - 173
38	X-RAY DIFFRACTION	38	B	174 - 180
39	X-RAY DIFFRACTION	39	B	181 - 228
40	X-RAY DIFFRACTION	40	B	229 - 242

-
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