PDB-4ys8: Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidyly...

ID or keywords:

Entry

Database: PDB / ID: 4ys8

Title

Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis

Components

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Keywords

TRANSFERASE / SSGCID / ispD / isoprenoid biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
Similarity search - Function

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.45 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis
Authors: Dranow, D.M. / Fairman, J.W. / Pierce, P.G. / Lorimer, D. / Edwards, T.E. / SSGCID

History

Deposition	Mar 16, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 8, 2015	Group: Other
Revision 1.2	Oct 28, 2015	Group: Database references
Revision 1.3	Oct 11, 2017	Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list / reflns_shell Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.4	Nov 3, 2021	Group: Data collection / Database references Category: database_2 / diffrn_detector ...database_2 / diffrn_detector / diffrn_radiation_wavelength / diffrn_source Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.5	Sep 27, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ys8.cif.gz	352.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ys8.ent.gz	288.5 KB	Display	PDB format
PDBx/mmJSON format	4ys8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ys8_validation.pdf.gz	479.2 KB	Display	wwPDB validaton report
Full document	4ys8_full_validation.pdf.gz	483.7 KB	Display
Data in XML	4ys8_validation.xml.gz	33.9 KB	Display
Data in CIF	4ys8_validation.cif.gz	46.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/4ys8 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/4ys8	HTTPS FTP

-
Related structure data

Related structure data	1vgwS S: Starting model for refinement
Similar structure data	5ddv-d 5dax-d 1inj-d 1g2m-d 6har-d 1i52-d 5dav-d 4h16-d 2boh-d 6jzm-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) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: SSGCID-ButhA.00168.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

hetero molecules

104 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

hetero molecules

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

2

B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

hetero molecules

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

3

C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

hetero molecules

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

4

D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

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

5

A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

hetero molecules

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

6

C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.650, 138.310, 78.590
Angle α, β, γ (deg.)	90.000, 101.890, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase / MCT Mass: 25821.379 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: ispD, BTH_I2089 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2SWT6, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#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-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.35 Å³/Da / Density % sol: 47.67 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: ButhA.00168.a.A1.PW33338 at 30.46 mg/ml was incuabted with 6mM MgCl2 and 6mM ATP, then mixed 1:1 with JCSG+(e11): 14.4% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.5, 160mM Calcium acetate, 20% glycerol

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2015 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.45→50 Å / Num. obs: 34999 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 37.04 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.077 / R_rim(I) all: 0.089 / Χ²: 0.966 / Net I/σ(I): 14.76 / Num. measured all: 134066

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
2.45-2.51		0.849	0.551	2.87	9986	2590	2593	0.64	100
2.51-2.58		0.874	0.466	3.24	9612	2499	2493	0.541	99.8
2.58-2.66		0.876	0.42	3.63	9555	2475	2480	0.488	100
2.66-2.74		0.914	0.345	4.31	9163	2377	2370	0.4	99.7
2.74-2.83		0.945	0.279	5.29	8932	2317	2315	0.324	99.9
2.83-2.93		0.96	0.226	6.65	8535	2218	2210	0.262	99.6
2.93-3.04		0.983	0.169	8.44	8373	2181	2177	0.196	99.8
3.04-3.16		0.989	0.124	10.79	7921	2058	2059	0.144	100
3.16-3.3		0.993	0.097	13.32	7644	1999	1994	0.113	99.7
3.3-3.46		0.994	0.076	16.96	7272	1892	1893	0.089	100
3.46-3.65		0.996	0.062	19.67	6817	1791	1785	0.073	99.7
3.65-3.87		0.997	0.05	22.85	6595	1731	1727	0.058	99.8
3.87-4.14		0.998	0.043	25.92	6244	1641	1642	0.05	100
4.14-4.47		0.998	0.037	30.12	5590	1469	1466	0.044	99.8
4.47-4.9		0.999	0.032	32.64	5265	1396	1390	0.038	99.6
4.9-5.48		0.998	0.035	31.57	4770	1250	1249	0.041	99.9
5.48-6.33		0.998	0.039	28.39	4225	1113	1110	0.045	99.7
6.33-7.75		0.999	0.029	33.7	3546	945	938	0.034	99.3
7.75-10.96		0.999	0.021	43.78	2705	730	724	0.025	99.2
	10.96	0.999	0.022	38.32	1316	414	384	0.026	92.8

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
MR-Rosetta		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VGW

1vgw

Resolution: 2.45→29.529 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2629	1744	4.99 %
R_work	0.2157	33173	-
obs	0.2181	34917	99.69 %

Solvent computation

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

Displacement parameters

B_iso max: 111.57 Å² / B_iso mean: 47.7916 Å² / B_iso min: 12.93 Å²

Refinement step

Cycle: final / Resolution: 2.45→29.529 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6617	0	34	205	6856
B_iso mean	-	-	71.19	41.02	-
Num. residues	-	-	-	-	887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6818
X-RAY DIFFRACTION	f_angle_d	0.78	9269
X-RAY DIFFRACTION	f_chiral_restr	0.037	1061
X-RAY DIFFRACTION	f_plane_restr	0.004	1224
X-RAY DIFFRACTION	f_dihedral_angle_d	11.716	2429

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.45-2.522	0.3346	149	0.281	2772	2921	99
2.522-2.6033	0.3018	133	0.272	2730	2863	100
2.6033-2.6963	0.3392	147	0.259	2828	2975	100
2.6963-2.8042	0.267	148	0.2525	2709	2857	100
2.8042-2.9317	0.3032	140	0.2519	2763	2903	100
2.9317-3.0861	0.3095	150	0.2451	2760	2910	100
3.0861-3.2792	0.2956	143	0.2438	2776	2919	100
3.2792-3.532	0.3026	158	0.2243	2750	2908	100
3.532-3.8868	0.27	138	0.2071	2776	2914	100
3.8868-4.4476	0.2141	146	0.1803	2763	2909	100
4.4476-5.5972	0.2074	146	0.1745	2784	2930	100
5.5972-29.5312	0.2281	146	0.1967	2762	2908	98

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	6.6366	-2.0038	1.2703	8.242	-1.525	3.7784	-0.1493	0.0907	-0.5809	-0.0342	0.0059	0.0393	0.0415	0.1862	0.1621	0.1622	-0.0326	0.0685	0.2559	-0.0234	0.2804	46.5237	85.9448	42.7634
2	3.1004	0.4469	0.1536	3.4916	-0.3895	5.4619	0.0127	-0.1211	-0.0559	-0.0066	-0.0245	-0.4132	-0.2038	0.4062	0.0055	0.1647	-0.0424	0.0359	0.2152	-0.0184	0.2795	47.1547	93.3784	46.7688
3	0.503	1.3724	-0.3703	4.9031	-0.7197	0.9887	0.0018	-0.0339	0.0837	0.2813	0.0366	0.4074	-0.0099	0.0158	-0.0295	0.1968	0.0003	-0.0061	0.2536	-0.0363	0.3095	30.713	81.9327	48.6686
4	5.227	-0.2631	-2.0271	6.4738	2.1414	2.0287	-0.061	-0.1671	-0.1472	0.2076	0.0352	-0.1621	0.2413	0.128	0.0122	0.3153	0.0128	0.0116	0.2825	0.0996	0.2035	35.5278	78.7997	47.6029
5	2.6389	-0.034	0.7877	4.0167	-1.7952	5.3432	-0.0082	0.2015	-0.2291	-0.0182	0.0745	0.0182	-0.2926	-0.0139	-0.1396	0.4299	0.0395	-0.0017	0.3114	0.0146	0.2856	31.4802	51.3249	33.0461
6	3.5965	1.5486	-0.5483	3.4066	0.6051	4.7514	-0.058	0.2402	0.1881	-0.3765	0.0143	0.2426	-0.235	-0.3324	-0.1172	0.361	0.0411	-0.0719	0.2351	-0.0316	0.2378	27.3089	45.8236	29.909
7	1.4648	-0.5931	0.5583	5.1238	-0.6701	3.4389	-0.0612	-0.0771	-0.2188	-0.0943	0.0348	0.327	0.4046	-0.2375	-0.0591	0.2382	-0.0048	0.023	0.2593	0.0027	0.184	27.5594	45.7182	40.8961
8	1.1989	0.1221	-0.0923	1.2927	0.1641	2.0628	-0.0666	-0.3875	-0.0508	0.5865	-0.0332	-0.0458	-0.0261	0.4969	0.0608	0.3025	0.0025	-0.0421	0.3096	-0.0211	0.3596	39.1313	50.9127	48.5056
9	0.4299	-0.6138	-0.0076	4.4233	0.2866	0.5221	-0.069	-0.1409	-0.1388	0.4496	-0.0673	0.8123	0.1866	-0.1472	0.0865	0.3422	-0.0387	0.0657	0.2772	0.0062	0.3447	25.6977	61.4698	51.5497
10	4.8515	-1.3631	0.0292	6.6165	-1.9692	4.2596	-0.0217	-0.4104	0.1014	0.4138	0.0537	0.5793	-0.1182	-0.2421	0.0117	0.3856	0.0497	0.0564	0.2118	-0.0853	0.2976	27.5986	56.5188	48.6875
11	4.7562	3.1046	-2.5737	4.6796	0.8002	7.4318	-0.3742	-0.0774	0.7739	-1.9036	0.6551	-0.7325	-0.6769	0.5496	-0.0892	0.7123	-0.1176	0.1329	0.3339	0.05	0.5118	33.94	68.1366	30.7859
12	4.1069	1.6751	1.4575	2.4629	-0.9818	1.8501	0.0032	0.2309	0.1582	0.0257	0.0716	0.0478	-0.0627	-0.2123	-0.0572	0.4296	-0.0183	-0.0408	0.3145	-0.0732	0.3014	23.589	107.2778	-8.5506
13	5.7195	0.3453	-0.3712	3.168	-1.4066	4.1606	-0.0742	0.4566	0.2538	-0.108	0.0016	-0.075	0.4327	-0.0566	0.0321	0.3811	0.0193	-0.0647	0.289	-0.0033	0.2868	24.5309	112.5855	-13.4789
14	2.2997	0.8857	0.4069	3.7558	0.4752	3.3918	-0.1504	0.0979	0.3213	-0.1113	-0.0179	-0.3843	-0.3866	0.0403	0.2049	0.4647	-0.0487	-0.169	0.228	-0.0385	0.3953	33.5622	116.7641	-4.8467
15	1.9744	1.3344	0.3795	2.2857	-0.7932	3.4842	0.2909	-0.455	0.0086	0.8951	-0.2639	-0.0265	0.2891	-0.4425	0.0513	0.4305	0.0256	-0.0389	0.3125	-0.0374	0.2402	27.5417	105.9856	5.0974
16	2.8582	0.6513	0.9995	8.4394	-1.9927	0.9461	-0.2497	0.0683	-0.5858	-1.176	-0.0267	-0.5842	0.0456	-0.001	0.013	0.4795	-0.0373	0.0299	0.2543	0.09	0.2466	41.0671	81.8743	0.5198
17	2.3743	-0.9867	-0.1965	2.4247	-0.5022	0.1969	-0.0332	-0.3927	-0.2892	0.2121	-0.2432	-0.321	-0.3794	0.0839	-0.1797	0.4899	-0.0314	-0.1776	0.3607	0.0353	0.228	39.1616	89.7384	6.0978
18	3.6629	1.498	-0.7703	8.9656	1.7093	9.3035	0.2266	0.5701	-0.2794	-0.2087	-0.401	-1.385	-0.617	0.3124	0.1697	0.4702	-0.0279	-0.1796	0.4046	-0.002	0.6653	41.7534	114.1505	-1.4933
19	8.8284	2.7665	2.0909	7.9528	1.708	4.0856	0.1317	-0.0682	-0.5772	0.2291	-0.061	-1.166	-0.0029	0.3113	-0.0752	0.3513	0.0445	-0.1301	0.2684	0.0676	0.4311	36.8457	102.1765	0.8649
20	2.9359	-2.1144	-1.4161	2.7138	2.593	2.7453	-0.1493	-0.679	-0.8461	0.0773	0.7664	0.627	0.9414	0.0193	-0.4006	0.5191	-0.0914	-0.0009	0.454	0.1227	0.5082	19.4818	90.9514	-8.2381
21	5.453	-1.2463	-0.9365	6.6179	-0.2992	2.7231	-0.0366	0.0684	0.2535	-0.3105	0.4121	1.1019	0.3777	-0.2833	-0.2995	0.4469	-0.081	-0.1029	0.3157	0.1677	0.5099	19.3511	68.4447	7.8635
22	2.5699	0.3248	-0.4547	6.1701	-0.8742	0.4527	0.0055	0.0621	-0.0612	-0.113	0.124	0.5688	0.0306	-0.0586	-0.1829	0.4851	-0.0427	-0.091	0.3291	0.0868	0.3049	25.3925	66.4838	7.2367
23	1.3163	-0.2395	0.2638	7.5835	0.743	0.5789	-0.3514	0.052	0.2401	0.0352	0.3371	-0.2894	0.1099	0.3245	0.0254	0.4687	-0.0693	-0.0585	0.3442	0.085	0.3262	38.9045	87.5602	2.8989
24	1.7241	-0.5798	-0.429	4.4252	-2.5444	2.9148	-0.0617	-0.2984	-0.0758	0.175	-0.178	-1.1402	-0.2131	0.4747	0.2051	0.4892	-0.0194	-0.1764	0.4387	0.1509	0.5973	40.0455	68.359	9.683
25	5.0913	-2.514	-3.05	5.264	3.7442	3.8623	-0.4625	0.7475	0.5969	-0.4746	-0.1282	0.3515	-0.0783	-0.375	0.3989	0.7377	-0.0089	-0.2186	0.3432	0.083	0.2979	28.011	82.3816	1.057
26	5.2718	-1.6287	-3.7508	9.3196	-2.6277	4.2958	-0.0377	0.2895	0.5769	1.1707	1.3396	1.5063	-0.4789	0.9432	-0.7574	0.5824	-0.0879	-0.1321	0.526	0.1077	0.5659	16.7543	88.8477	5.3513

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 43 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 96 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 185 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 186 through 231 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -1 through 43 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 44 through 81 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 82 through 115 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 116 through 138 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 139 through 185 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 186 through 218 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 219 through 230 )	B
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 0 through 43 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 44 through 81 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 82 through 107 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 108 through 138 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 139 through 152 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 153 through 168 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 169 through 186 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 187 through 218 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 219 through 231 )	C
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1 through 65 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 66 through 126 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 127 through 168 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 169 through 204 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 205 through 218 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 219 through 230 )	D

-
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