PDB-4x2c: Clostridium difficile Fic protein_0569 mutant S31A, E35A

ID or keywords:

Entry

Database: PDB / ID: 4x2c

Title

Clostridium difficile Fic protein_0569 mutant S31A, E35A

Components

Fic family protein putative filamentation induced by cAMP protein

Keywords

STRUCTURAL PROTEIN / Fic protein / a-helical / SE/AA mutant

Function / homology

Function and homology information

ATP binding / metal ion binding
Similarity search - Function

Biological species

Peptoclostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Jorgensen, R. / Dedic, E.

Funding support

Denmark, 1items

Citation

Journal: To Be Published
Title: Structure of Clostridium difficile Fic_0569 S31A, E35A mutant at 1.8 Angstroms resolution
Authors: Jorgensen, R. / Dedic, E. / Alsarraf, H. / Welner, D. / Leeuwen, H.C. / Oestergaard, O.

History

Deposition	Nov 26, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2018	Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4x2c.cif.gz	195.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4x2c.ent.gz	158.5 KB	Display	PDB format
PDBx/mmJSON format	4x2c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/4x2c ftp://data.pdbj.org/pub/pdb/validation_reports/x2/4x2c	HTTPS FTP

-
Related structure data

Related structure data	4x2dC 3cucS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x2d-3 4x2e-3 4x2e-2 4x2e-1 4x2d-2 1ioa-d 4x2d-1 3p4x-1 1jep-5 4x2d-4 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: Fic family protein putative filamentation induced by cAMP protein

B: Fic family protein putative filamentation induced by cAMP protein

hetero molecules

55.4 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)	52.370, 67.290, 139.600
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Fic family protein putative filamentation induced by cAMP protein Mass: 27296.156 Da / Num. of mol.: 2 / Mutation: S31A, E35A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: R20291 / Gene: CDR20291_0569 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C9YJ22
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.19 Å³/Da / Density % sol: 43.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M MgCl2-6xH2O 25.0 % (w/v) PEG 3350, 0.1 M HEPES pH 7.5

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

MAX II

/ Beamline: I911-2 / Wavelength: 1.03841 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 11, 2014
Details: Multilayer mirror, curved to focus in the vertical (R = 400 m)

Radiation

Monochromator: Bent Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03841 Å / Relative weight: 1

Reflection

Resolution: 1.8→19.12 Å / Num. obs: 46011 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 26.25 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.07 / R_rim(I) all: 0.077 / Χ²: 0.911 / Net I/σ(I): 19.04 / Num. measured all: 301559

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.8-1.9		0.779	0.881	2.3	43614	6856	6663	0.957	97.2
1.9-2		0.895	0.516	4.08	36420	5571	5483	0.56	98.4
2-2.2		0.96	0.285	7.3	54717	8351	8240	0.31	98.7
2.2-2.5		0.99	0.137	14.57	53202	8114	8042	0.149	99.1
2.5-2.8		0.996	0.08	22.27	32842	4985	4961	0.087	99.5
2.8-3		0.998	0.058	27.46	15220	2319	2312	0.063	99.7
3-4		0.999	0.038	40.22	38452	5927	5910	0.041	99.7
4-5		0.999	0.027	56.91	13579	2140	2137	0.03	99.9
5-6		0.999	0.027	54.32	5986	963	962	0.029	99.9
6-10		0.999	0.024	58.02	6335	1082	1061	0.027	98.1
	10	0.999	0.022	58.28	1192	342	240	0.024	70.2

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	19.12 Å
Translation	2.5 Å	19.12 Å

-
Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
PHASER	2.3.0	phasing
PDB_EXTRACT	3.15	data extraction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3cuc

3cuc

Resolution: 1.8→19.1 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2182	1378	3 %	Random selection
R_work	0.1812	44575	-	-
obs	0.1823	45953	98.82 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 153.91 Å² / B_iso mean: 37.758 Å² / B_iso min: 12.24 Å²

Refinement step

Cycle: final / Resolution: 1.8→19.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3395	0	50	216	3661
B_iso mean	-	-	62.29	40.66	-
Num. residues	-	-	-	-	410

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3598
X-RAY DIFFRACTION	f_angle_d	0.999	4877
X-RAY DIFFRACTION	f_chiral_restr	0.04	544
X-RAY DIFFRACTION	f_plane_restr	0.005	612
X-RAY DIFFRACTION	f_dihedral_angle_d	13.124	1335

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8004-1.8647	0.3618	133	0.2966	4306	4439	97
1.8647-1.9393	0.2791	136	0.2438	4364	4500	98
1.9393-2.0274	0.2655	135	0.2243	4388	4523	99
2.0274-2.1342	0.2697	137	0.1927	4414	4551	99
2.1342-2.2677	0.2235	137	0.1775	4418	4555	99
2.2677-2.4425	0.2153	136	0.1684	4454	4590	99
2.4425-2.6877	0.1871	139	0.1691	4473	4612	99
2.6877-3.0752	0.2023	139	0.1667	4509	4648	100
3.0752-3.8691	0.1912	142	0.1614	4556	4698	100
3.8691-19.1006	0.2166	144	0.1834	4693	4837	99

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	3.4762	3.6259	-5.3254	4.0792	-5.7219	8.2732	0.103	0.8875	-0.4461	-0.6273	-0.1354	-0.7184	0.7969	0.4115	0.0431	0.46	0.1073	-0.0187	0.4267	-0.0382	0.3709	45.0486	49.2461	37.0752
2	4.1064	-1.6379	-1.0036	3.1875	3.2059	5.0635	0.1476	0.2639	0.1056	-0.2451	-0.0093	-0.1666	-0.1474	0.0159	-0.1159	0.1922	-0.0314	-0.0272	0.2145	0.042	0.2501	42.2735	58.8729	41.6549
3	1.5656	2.0457	-1.7896	5.136	0.4711	6.44	0.0425	0.0703	0.1679	0.1084	-0.0587	0.3406	-0.1795	-0.3859	0.0146	0.1346	0.0087	-0.0222	0.2233	0.0188	0.2358	38.3519	66.8137	51.5483
4	0.7444	-1.0567	-0.917	3.7918	4.4857	7.1594	0.1344	0.0618	0.3268	-0.6053	0.0979	-0.1674	-0.2218	-0.0757	-0.1939	0.1574	-0.0119	0.0028	0.2786	-0.0172	0.2951	45.6959	72.9713	47.2163
5	2.1121	-0.4949	0.0518	7.5714	4.8423	4.9171	0.1558	-0.0645	0.0708	0.3433	0.0556	-0.687	0.181	0.2393	-0.2583	0.2011	-0.021	-0.0517	0.2566	0.0527	0.2467	48.9753	61.2352	52.6569
6	3.3132	-4.7484	-0.7406	6.9244	1.6842	3.3974	0.5015	0.176	-1.0785	-0.1774	0.1565	-0.4426	1.6593	0.2938	-0.5492	0.5471	0.0397	-0.1179	0.3155	0.0604	0.6562	50.1183	41.8807	54.1669
7	2.2624	1.8695	0.0382	2.2916	-1.21	2.1213	0.023	-0.3668	-0.6828	0.8824	-0.3379	-0.5346	0.3801	0.4539	0.4638	0.4017	0.0404	-0.0879	0.3471	0.0646	0.458	52.6123	48.8549	61.1584
8	3.3061	3.2725	-0.3046	3.3569	-0.207	2.0827	0.126	-0.5822	0.5965	0.7332	0.032	-0.889	0.0653	0.6224	-0.1499	0.305	0.0148	-0.0555	0.3649	0.0377	0.4232	53.162	62.1958	60.8197
9	6.3544	1.834	-1.8755	2.4603	2.2506	4.5959	0.2334	-0.9112	-0.4367	0.6676	0.6274	0.2794	1.2157	-0.6767	-1.0951	0.7589	-0.0318	-0.1026	0.8046	0.2188	0.9237	46.9886	47.2534	76.4177
10	7.9225	4.1212	2.6209	4.4852	5.8617	9.4915	0.2616	-0.9875	-1.2175	0.7849	0.37	-0.0329	0.8697	0.2087	-0.4681	0.4964	-0.0303	-0.1448	0.386	0.1678	0.4891	44.1118	39.7875	66.5842
11	4.4641	-3.101	0.2349	2.6295	-1.0163	1.558	0.1209	0.0178	-0.4653	0.1583	0.053	0.4916	0.3694	-0.4571	-0.1957	0.5282	-0.167	-0.1385	0.3496	0.0782	0.5398	38.1834	36.7082	56.3017
12	3.6577	-0.3415	0.0944	2.8659	-0.8376	4.3122	0.078	-0.2535	-0.364	0.3153	0.0356	0.0893	0.3579	-0.3681	-0.1046	0.4332	-0.1095	-0.0483	0.3013	0.0878	0.2475	38.0847	47.3187	64.4444
13	3.127	-3.7119	3.8093	5.2811	-2.7578	8.374	-0.4869	-0.512	0.6862	0.9598	-0.3854	-0.3234	-0.9519	0.378	0.7828	0.4839	-0.0795	-0.0846	0.3185	0.0141	0.3148	45.1353	57.4102	64.8093
14	2.5502	-0.9312	-1.2424	8.2409	4.3749	8.5299	0.1039	0.0144	-0.2514	0.5113	-0.0019	0.0355	0.9491	-0.3668	-0.1157	0.2932	-0.0425	-0.0693	0.1958	0.0335	0.242	41.1979	47.9806	52.6489
15	1.3225	-1.2245	0.8584	7.9846	6.2694	8.353	0.0403	-0.0296	0.1383	0.6431	-0.0265	0.4533	0.0241	-0.5695	0.0248	0.3256	-0.0953	0.0948	0.3241	0.0552	0.3046	30.9502	56.2149	51.9944
16	8.4292	-4.3121	-1.0142	4.3578	-2.3631	6.9531	0.5066	-0.7151	1.2385	1.2742	-0.5707	0.666	-0.4031	-0.3749	0.0131	0.4022	-0.1641	0.128	0.4699	-0.1029	0.4981	28.9464	56.8647	62.176
17	5.7593	0.8327	-1.5601	4.5057	-1.0747	0.5919	0.0031	-1.102	-0.6984	0.4392	0.2512	0.3592	0.7128	-0.9191	-0.2544	0.5544	-0.2554	0.0189	0.7183	0.1389	0.4172	27.7321	45.9883	64.41
18	9.7865	-4.1924	-4.5031	2.1318	2.0237	2.0974	-0.0266	0.37	-0.3031	0.0957	-0.0482	0.3809	0.9934	-1.5238	-0.0951	0.3436	-0.2069	0.0067	0.4442	0.0101	0.3365	26.9676	50.8083	51.0504
19	8.8568	-4.3245	0.9776	3.8046	1.1442	5.0032	0.199	0.2161	-0.0483	0.1277	-0.2574	0.3549	0.815	-0.8443	0.0963	0.2948	-0.101	-0.0363	0.3194	-0.0205	0.1811	32.2305	51.8965	39.8558
20	4.0485	-4.558	-1.8634	6.2671	3.2987	5.1958	0.0489	-0.1118	-0.4881	0.0438	-0.2634	0.2327	0.2476	-0.8288	0.1378	0.2403	-0.0556	-0.0704	0.3146	0.0126	0.2468	35.1772	50.7298	31.6214
21	9.742	-2.3443	2.0749	3.6211	-3.6618	3.7139	-1.0727	-1.1846	0.1443	1.0919	0.3909	0.0325	0.4158	0.5113	0.5388	1.0867	-0.1636	0.0385	0.6983	-0.0768	0.3227	68.2521	94.0958	70.5797
22	6.8035	1.6507	-5.0669	6.4663	-0.6733	7.3468	0.4779	-0.9785	-0.1742	0.8439	-0.1879	0.3209	0.3332	0.1001	-0.116	1.1948	-0.0508	0.3877	1.1747	0.5416	1.0016	60.944	88.1414	72.8246
23	4.2307	-2.0987	4.2619	1.6109	-1.4739	7.7011	0.2128	-0.665	0.2789	0.9962	-0.0716	0.7031	-0.7513	-0.4448	-0.169	0.5542	-0.1362	0.1775	0.3478	-0.0281	0.359	59.0645	90.4696	61.0786
24	7.7255	7.7961	-0.4505	8.8702	0.9059	9.4597	0.1219	0.2996	0.1344	-0.1952	0.0669	0.3603	-0.0633	-0.2326	-0.2244	0.1855	-0.0037	-0.0004	0.1714	0.016	0.2247	58.6164	85.6416	47.6265
25	4.2038	0.0975	-1.3448	8.9576	-1.6369	8.5262	0.7531	-0.1779	1.3327	0.4902	-0.2957	0.7713	-1.1713	0.122	-0.3173	0.3088	-0.0418	0.1121	0.2453	-0.0471	0.4508	50.4375	86.5353	55.2067
26	5.8948	3.2127	2.0345	9.1407	1.3643	2.107	0.3415	-0.3661	0.5795	0.4451	-0.2233	0.2535	-0.4673	0.2433	-0.1784	0.2506	-0.0191	0.0488	0.2564	-0.0381	0.2923	48.8248	80.6388	57.3142
27	6.5171	2.2751	2.9585	3.3703	0.5338	3.6196	0.312	-0.3838	-0.4346	0.611	-0.2153	-0.0786	-0.1394	-0.0073	-0.1069	0.2617	-0.0622	0.0021	0.2203	0.0671	0.2293	60.2009	78.6388	55.8301
28	3.7917	-0.5672	-0.2337	3.1447	4.296	5.951	0.2437	-0.8225	-0.6204	1.4989	-0.0593	-0.6567	0.8118	0.2534	-0.1785	0.6222	-0.1737	-0.1423	0.6123	0.0368	0.3705	75.1903	84.2038	66.1736
29	8.5497	-0.2575	0.579	5.4229	1.8602	3.5332	0.7562	0.0853	-1.0509	0.7739	-0.4075	-0.8548	0.4671	0.417	-0.4345	0.3733	-0.0805	-0.2079	0.5196	0.15	0.5236	79.9824	78.5401	58.2227
30	7.6186	-0.9259	0.8334	1.6478	-0.2609	5.238	0.4317	0.0871	-1.3123	0.5117	-0.3446	-0.462	0.3332	0.2707	-0.0294	0.2713	-0.0149	-0.1085	0.2182	0.0795	0.4198	67.7001	73.1133	53.4475
31	4.5925	4.7997	4.0076	7.0026	3.4801	3.7825	0.178	0.7297	-0.2733	0.15	-0.205	-0.8266	0.6431	1.2398	0.0487	0.2536	0.0743	-0.0426	0.4213	0.0745	0.4839	85.3986	77.4377	46.8386
32	3.67	0.2013	0.7163	0.5025	-0.0778	0.6956	0.0106	-0.2981	0.0515	0.2733	0.0208	-0.4261	-0.5025	0.5657	-0.074	0.2007	-0.3689	-0.3343	0.5827	0.1396	0.4271	86.8295	89.142	54.8258
33	4.9325	-1.0632	0.4435	0.3791	-0.2405	2.9325	0.1987	-0.0996	0.1429	0.2722	-0.2991	-0.4215	-0.5023	0.5384	0.0082	0.2425	-0.1142	-0.0446	0.2869	0.0657	0.2207	78.7488	89.159	47.9697
34	4.2175	-3.5069	-2.9996	3.3679	1.8796	3.0273	0.1479	0.2433	-1.3064	-0.2732	-0.4609	0.8192	0.4287	-0.6951	0.2505	0.2282	-0.0386	-0.0536	0.2883	-0.0117	0.4149	70.9763	76.6238	45.6494
35	4.9459	0.0728	2.9663	4.1749	2.0381	9.1021	0.4289	-0.3055	-0.2118	0.4549	-0.1616	-0.242	-0.4696	0.0694	-0.2723	0.2541	-0.0889	-0.0024	0.2463	0.0542	0.2099	70.7188	87.2519	54.5044
36	5.8512	-0.1553	4.3154	4.1617	2.0333	5.1719	-0.0887	-0.4689	0.472	0.3146	-0.1558	0.2499	-0.9722	0.0186	0.3736	0.391	-0.186	0.0218	0.3233	0.0075	0.1615	68.5358	95.6296	55.3304
37	6.7463	-0.1171	-1.4311	3.7426	-0.2633	3.2435	0.2786	0.3107	0.305	-0.0192	-0.2464	-0.1097	-0.6483	0.2833	-0.0247	0.33	-0.0525	0.0054	0.2356	0.0556	0.1733	72.8694	95.6101	41.6237
38	7.5958	-0.0556	-3.1693	4.7954	2.2974	2.8183	1.0839	-0.4319	0.5637	0.409	-0.3529	-0.0073	-1.6122	0.3109	-0.709	0.6259	-0.1279	0.0859	0.2685	-0.0255	0.3404	68.0671	101.4562	52.5421
39	0.7072	-0.2076	0.0662	1.3645	1.0964	1.1027	0.0044	-0.1619	0.2874	0.3321	0.3697	-0.411	-0.0928	0.398	0.0065	1.179	-0.1935	0.1857	0.2288	-0.3433	0.3183	63.9259	100.9816	61.9034
40	4.4849	-4.76	-2.5343	5.0552	2.539	6.5089	-0.1672	-0.4772	0.3326	0.2914	-0.2148	0.1497	0.0711	-0.524	0.4272	1.3579	-0.2686	0.3212	0.4738	-0.2096	0.5521	62.6845	102.3358	68.5406

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 4:14)	A	4 - 14
2	X-RAY DIFFRACTION	2	(chain A and resid 15:28)	A	15 - 28
3	X-RAY DIFFRACTION	3	(chain A and resid 29:45)	A	29 - 45
4	X-RAY DIFFRACTION	4	(chain A and resid 46:56)	A	46 - 56
5	X-RAY DIFFRACTION	5	(chain A and resid 57:79)	A	57 - 79
6	X-RAY DIFFRACTION	6	(chain A and resid 80:84)	A	80 - 84
7	X-RAY DIFFRACTION	7	(chain A and resid 85:91)	A	85 - 91
8	X-RAY DIFFRACTION	8	(chain A and resid 92:100)	A	92 - 100
9	X-RAY DIFFRACTION	9	(chain A and resid 126:131)	A	126 - 131
10	X-RAY DIFFRACTION	10	(chain A and resid 132:140)	A	132 - 140
11	X-RAY DIFFRACTION	11	(chain A and resid 141:150)	A	141 - 150
12	X-RAY DIFFRACTION	12	(chain A and resid 151:164)	A	151 - 164
13	X-RAY DIFFRACTION	13	(chain A and resid 165:171)	A	165 - 171
14	X-RAY DIFFRACTION	14	(chain A and resid 172:185)	A	172 - 185
15	X-RAY DIFFRACTION	15	(chain A and resid 186:196)	A	186 - 196
16	X-RAY DIFFRACTION	16	(chain A and resid 197:204)	A	197 - 204
17	X-RAY DIFFRACTION	17	(chain A and resid 205:215)	A	205 - 215
18	X-RAY DIFFRACTION	18	(chain A and resid 216:223)	A	216 - 223
19	X-RAY DIFFRACTION	19	(chain A and resid 224:228)	A	224 - 228
20	X-RAY DIFFRACTION	20	(chain A and resid 229:235)	A	229 - 235
21	X-RAY DIFFRACTION	21	(chain B and resid 4:10)	B	4 - 10
22	X-RAY DIFFRACTION	22	(chain B and resid 11:15)	B	11 - 15
23	X-RAY DIFFRACTION	23	(chain B and resid 16:30)	B	16 - 30
24	X-RAY DIFFRACTION	24	(chain B and resid 31:38)	B	31 - 38
25	X-RAY DIFFRACTION	25	(chain B and resid 39:46)	B	39 - 46
26	X-RAY DIFFRACTION	26	(chain B and resid 47:56)	B	47 - 56
27	X-RAY DIFFRACTION	27	(chain B and resid 57:76)	B	57 - 76
28	X-RAY DIFFRACTION	28	(chain B and resid 77:81)	B	77 - 81
29	X-RAY DIFFRACTION	29	(chain B and resid 82:87)	B	82 - 87
30	X-RAY DIFFRACTION	30	(chain B and resid 88:100)	B	88 - 100
31	X-RAY DIFFRACTION	31	(chain B and resid 129:135)	B	129 - 135
32	X-RAY DIFFRACTION	32	(chain B and resid 136:146)	B	136 - 146
33	X-RAY DIFFRACTION	33	(chain B and resid 147:164)	B	147 - 164
34	X-RAY DIFFRACTION	34	(chain B and resid 165:169)	B	165 - 169
35	X-RAY DIFFRACTION	35	(chain B and resid 170:182)	B	170 - 182
36	X-RAY DIFFRACTION	36	(chain B and resid 183:194)	B	183 - 194
37	X-RAY DIFFRACTION	37	(chain B and resid 195:217)	B	195 - 217
38	X-RAY DIFFRACTION	38	(chain B and resid 218:223)	B	218 - 223
39	X-RAY DIFFRACTION	39	(chain B and resid 224:228)	B	224 - 228
40	X-RAY DIFFRACTION	40	(chain B and resid 229:233)	B	229 - 233

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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