PDB-4n8g: Crystal structure of a TRAP periplasmic solute binding protein fr...

ID or keywords:

Entry

Database: PDB / ID: 4n8g

Title

Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0660), Target EFI-501075, with bound D-alanine-D-alanine

Components

TRAP dicarboxylate transporter, DctP subunit

Keywords

TRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics

Function / homology

Function and homology information

transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Chromohalobacter salexigens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.502 Å

Authors

Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...

Citation

Journal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...

History

Deposition	Oct 17, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 25, 2015	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4n8g.cif.gz	735.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4n8g.ent.gz	648.4 KB	Display	PDB format
PDBx/mmJSON format	4n8g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4n8g_validation.pdf.gz	478.7 KB	Display	wwPDB validaton report
Full document	4n8g_full_validation.pdf.gz	484.5 KB	Display
Data in XML	4n8g_validation.xml.gz	57.9 KB	Display
Data in CIF	4n8g_validation.cif.gz	89.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n8/4n8g ftp://data.pdbj.org/pub/pdb/validation_reports/n8/4n8g	HTTPS FTP

-
Related structure data

Related structure data	4ln5C 4mcoC 4mevC 4mhfC 4mijC 4mncC 4mniC 4mx6C 4n15C 4n17C 4n4uC 4n6dC 4n6kC 4n8yC 4n91C 4napC 4nf0C 4ng7C 4nguC 4nhbC 4nn3C 4nq8C 4nx1C 4o7mC 4o8mC 4o94C 4oa4C 4oanC 4ovpC 4ovqC 4ovrC 4ovsC 4ovtC 4p1eC 4p1lC 4p3lC 4p47C 4p56C 4p8bC 4p9kC 4pafC 4paiC 4pakC 4pbhC 4pbqC 4pc9C 4pcdC 4pddC 4pdhC 4pe3C 4petC 4pf6C 4pf8C 4pfbC 4pfiC 4pfrC 4pgnC 4pgpC 4uabC C: citing same article (ref.)
Similar structure data	1os7-d 5txl-1 4cqn-2 2rka-d 4cqn-1 3bsc-d 6kdn-1 6fjy-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: EFI-510075

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TRAP dicarboxylate transporter, DctP subunit

B: TRAP dicarboxylate transporter, DctP subunit

C: TRAP dicarboxylate transporter, DctP subunit

D: TRAP dicarboxylate transporter, DctP subunit

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: TRAP dicarboxylate transporter, DctP subunit

hetero molecules

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

3

B: TRAP dicarboxylate transporter, DctP subunit

hetero molecules

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

4

C: TRAP dicarboxylate transporter, DctP subunit

hetero molecules

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

5

D: TRAP dicarboxylate transporter, DctP subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.536, 67.964, 276.012
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	TRAP dicarboxylate transporter, DctP subunit / TRAP periplasmic solute binding protein Mass: 40153.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_0660 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1QZT7
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-DAL / D-ALANINE Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₇NO₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1382 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	THIS ENTRY CONTAINS THE LIGAND D-ALANINE-D-ALANINE.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.91 Å³/Da / Density % sol: 35.72 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 10 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Ala-D-Ala, reservoir: 0.2 M sodium chloride, 0.1 M acetate, pH 4.5, 1.26 M ammonium sulfate, cryoprotection: 4:1 2.0 M lithium ...Details: 10 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Ala-D-Ala, reservoir: 0.2 M sodium chloride, 0.1 M acetate, pH 4.5, 1.26 M ammonium sulfate, cryoprotection: 4:1 2.0 M lithium sulfate:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal

Density Matthews: 1.91 Å³/Da / Density % sol: 35.72 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 10 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Ala-D-Ala, reservoir: 0.2 M sodium chloride, 0.1 M acetate, pH 4.5, 1.26 M ammonium sulfate, cryoprotection: 4:1 2.0 M lithium ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 10, 2013 / Details: mirrors

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.502→138.006 Å / Num. all: 197113 / Num. obs: 196106 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / B_iso Wilson estimate: 14.62 Å² / R_merge(I) obs: 0.092 / R_sym value: 0.092 / Χ²: 1.228 / Net I/σ(I): 6.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.502-1.53	7.5	0.779	19017	0.794	1	100
1.53-1.55	7.5	0.696	18985	0.813	1	100
1.55-1.58	7.6	0.577	19001	0.825	1	100
1.58-1.62	7.6	0.502	18927	0.838	1	100
1.62-1.65	7.6	0.432	19001	0.848	1	100
1.65-1.69	7.6	0.379	18965	0.862	1	100
1.69-1.73	7.6	0.323	18965	0.878	1	100
1.73-1.78	7.6	0.278	19056	0.892	1	100
1.78-1.83	7.6	0.233	18867	0.919	1	100
1.83-1.89	7.5	0.228	19066	0.984	1	100
1.89-1.96	7.5	0.194	18939	1.589	1	100
1.96-2.04	7.7	0.127	18988	0.997	1	100
2.04-2.13	7.6	0.102	18995	1.045	1	100
2.13-2.24	6.7	0.118	18036	1.569	1	94.9
2.24-2.38	6.8	0.118	18737	2.084	1	99.2
2.38-2.56	7.3	0.097	19010	2.135	1	100
2.56-2.82	7	0.088	18998	2.388	1	100
2.82-3.23	7	0.065	18926	1.906	1	99.7
3.23-4.07	6.2	0.043	18480	1.539	1	97.2
4.07-100	6.6	0.031	18546	1.079	1	97.6

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data reduction
SHELXS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.502→30.869 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.9051 / SU ML: 0.13 / σ(F): 0 / σ(I): 0 / Phase error: 16.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.181	9813	5.03 %	RANDOM
R_work	0.1586	-	-	-
all	0.1598	194898	-	-
obs	0.1598	194898	98.88 %	-

Solvent computation

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

Displacement parameters

B_iso max: 77.9 Å² / B_iso mean: 19.8039 Å² / B_iso min: 7.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.502→30.869 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10141	0	53	1382	11576

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10486
X-RAY DIFFRACTION	f_angle_d	1.234	14260
X-RAY DIFFRACTION	f_chiral_restr	0.074	1526
X-RAY DIFFRACTION	f_plane_restr	0.006	1931
X-RAY DIFFRACTION	f_dihedral_angle_d	13.601	3928

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.502-1.519	0.248	288	0.202	6012	6300	96
1.519-1.5369	0.2217	312	0.1834	6156	6468	100
1.5369-1.5556	0.2198	343	0.1811	6152	6495	100
1.5556-1.5753	0.2109	338	0.1694	6181	6519	100
1.5753-1.596	0.1795	344	0.1623	6138	6482	100
1.596-1.6179	0.1923	337	0.1609	6142	6479	100
1.6179-1.641	0.1879	337	0.1525	6189	6526	100
1.641-1.6655	0.1787	361	0.1479	6113	6474	100
1.6655-1.6915	0.1813	323	0.1478	6209	6532	100
1.6915-1.7193	0.1801	337	0.1458	6205	6542	100
1.7193-1.7489	0.1717	295	0.1467	6208	6503	100
1.7489-1.7807	0.1835	322	0.1397	6200	6522	100
1.7807-1.815	0.1906	342	0.1394	6150	6492	100
1.815-1.852	0.1772	338	0.1416	6193	6531	100
1.852-1.8923	0.2231	309	0.1983	5942	6251	95
1.8923-1.9363	0.3097	306	0.2877	5926	6232	95
1.9363-1.9847	0.184	286	0.1641	6096	6382	97
1.9847-2.0383	0.1833	315	0.1374	6204	6519	100
2.0383-2.0983	0.1496	321	0.1294	6252	6573	100
2.0983-2.166	0.1643	322	0.1368	6185	6507	100
2.166-2.2434	0.203	310	0.2016	5776	6086	92
2.2434-2.3332	0.2336	340	0.2075	5956	6296	96
2.3332-2.4394	0.1408	306	0.128	6286	6592	100
2.4394-2.5679	0.1672	336	0.1402	6233	6569	100
2.5679-2.7287	0.1671	346	0.1434	6314	6660	100
2.7287-2.9392	0.1611	331	0.1509	6263	6594	100
2.9392-3.2347	0.1714	357	0.1528	6300	6657	100
3.2347-3.7021	0.1687	323	0.1511	6256	6579	98
3.7021-4.6617	0.1455	336	0.1296	6310	6646	98
4.6617-30.8751	0.1933	352	0.1842	6538	6890	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	1.142	-0.6492	0.286	1.1514	-0.0467	0.5674	-0.0053	-0.1203	-0.059	0.1879	-0.0715	-0.2091	0.0639	0.1477	0.0588	0.1437	-0.0091	-0.028	0.1437	0.0333	0.1306	14.2934	27.3621	135.393
2	0.8397	0.3433	0.0625	0.7571	-0.2921	0.5633	-0.0656	0.0712	-0.043	-0.0088	0.0313	-0.0774	0.0125	0.0689	0.0342	0.1021	-0.013	0.0165	0.1075	-0.0083	0.1151	7.7626	28.3317	118.7794
3	1.0082	0.0002	-0.1771	0.884	-0.5643	0.9547	-0.0173	0.0104	0.0579	0.0613	0.0393	0.0249	-0.0412	-0.0049	-0.0101	0.1378	-0.0214	0.0181	0.1135	-0.0126	0.1273	-11.5585	35.5973	124.9434
4	1.397	0.0336	-0.0717	0.5137	-0.3127	0.8858	-0.0912	0.0041	-0.0905	-0.0029	-0.0233	-0.1168	0.0539	0.1374	0.082	0.1047	-0.0121	0.0171	0.1093	0.0023	0.1284	10.8229	26.7561	122.3535
5	3.0293	-0.1319	-0.5722	0.5873	-0.0988	0.8523	-0.049	-0.078	-0.2782	0.0844	-0.0254	-0.0325	0.1031	0.1165	0.0709	0.1587	0.0049	0.0143	0.1085	0.0142	0.1301	5.1354	19.3135	131.5643
6	0.596	-0.0223	0.0949	0.4828	-0.0109	0.461	-0.0034	0.0693	0.0165	0.0569	0.0802	0.1311	0.1197	-0.1627	-0.0209	0.1528	-0.0595	0.0054	0.1615	-0.0017	0.1591	-15.2753	25.6683	116.9595
7	1.0864	-0.0066	0.1225	0.6658	-0.1695	0.7218	0.0618	0.2484	-0.1529	-0.1687	0.0274	0.1704	0.0755	-0.0415	-0.0665	0.2091	-0.0444	0.0285	0.2343	-0.0216	0.2204	-4.2866	23.186	102.7664
8	1.2258	0.3877	-0.2813	0.9832	-0.2398	1.6697	-0.0542	0.2341	0.0532	-0.2212	0.1189	0.0719	-0.0938	-0.1665	-0.0565	0.1194	-0.0257	-0.018	0.1564	0.0219	0.1326	-5.0727	56.6322	97.21
9	0.4325	-0.1806	0.0265	0.5508	0.0261	1.0249	0.0185	0.0424	-0.0085	-0.0402	-0.0006	-0.0142	-0.0104	0.0117	-0.0169	0.0959	-0.0227	0.0073	0.0954	0.0002	0.1108	9.1906	51.1114	106.7846
10	0.2421	-0.1617	-0.0565	0.9628	0.3709	0.7228	-0.0071	-0.0119	-0.0059	0.1171	-0.0187	0.0896	0.0001	-0.0158	0.0222	0.1367	-0.0322	0.0207	0.1179	0.0029	0.1433	3.0464	57.5106	120.484
11	0.6943	-0.0491	-0.3147	1.093	1.0151	2.7905	0.0479	0.0975	0.113	-0.2153	0.0534	0.0128	-0.2844	0.1097	-0.102	0.1429	-0.0357	-0.0039	0.1051	0.0148	0.1426	2.9769	64.9838	101.6563
12	0.121	-0.0547	-0.1741	0.6895	0.2333	0.3569	-0.0696	-0.0634	0.1446	0.2838	0.0382	-0.0614	-0.1038	0.0389	0.0192	0.1912	-0.0578	-0.0334	0.1558	-0.0249	0.175	13.4185	64.4129	125.4187
13	0.6786	0.4701	-0.5306	1.8319	-0.2963	0.4198	0.0518	-0.231	-0.0887	0.3632	-0.2346	-0.4182	-0.3457	0.6623	0.038	0.2261	-0.1145	-0.0304	0.3301	0.0395	0.2397	26.2251	53.6592	115.2177
14	1.3577	0.0887	-0.2366	0.9479	-0.2012	1.1704	0.005	0.0776	-0.0938	-0.0754	-0.0128	0.2499	0.1565	-0.3084	0.0127	0.1456	-0.0657	0.0059	0.187	-0.0315	0.1398	13.438	8.5933	85.1017
15	0.6613	-0.0212	0.1496	0.8369	-0.0375	0.5958	0.0101	-0.0334	0.0148	0.0468	-0.0319	0.043	0.0665	-0.1441	0.0198	0.1064	-0.044	0.0228	0.132	-0.0107	0.1115	23.1487	16.7289	98.046
16	0.6012	0.0941	0.1635	1.0839	0.271	0.9229	0.0243	0.0322	0.0223	0.02	-0.0233	-0.049	0.1175	0.0172	0.0101	0.1389	-0.0081	0.0133	0.1274	0.008	0.1222	41.9828	10.1204	90.3011
17	1.3511	-0.4604	0.0366	0.7459	-0.0687	0.5437	0.0453	-0.0462	-0.1012	-0.0047	-0.0288	0.152	0.1784	-0.1507	-0.0033	0.1795	-0.0699	0.013	0.1406	-0.0022	0.1054	19.5545	6.6441	94.6111
18	0.8527	-0.5697	-0.1541	0.9931	0.0833	0.5087	0.021	-0.0287	-0.0886	0.1432	-0.0359	-0.1437	0.262	0.1623	0.0165	0.2384	0.0195	-0.0206	0.1943	0.02	0.1696	43.5289	7.0939	103.6352
19	1.8288	1.5115	-0.954	1.5885	-0.3083	1.2931	0.1315	-0.5098	-0.043	0.1992	-0.2508	0.0336	-0.079	0.0562	0.0975	0.2218	-0.034	-0.0098	0.2966	0.0088	0.2151	31.0931	17.5503	113.5382
20	0.709	0.1484	0.4581	0.9838	0.4238	0.8298	0.0307	-0.0163	0.0442	0.1351	-0.0108	-0.0732	-0.0058	0.0941	-0.0193	0.1036	-0.0387	-0.0181	0.1401	0.0182	0.1377	48.3827	43.8387	100.1504
21	0.775	0.1011	0.2274	0.6068	0.0994	0.9141	0.0039	-0.119	0.0618	0.0755	-0.0429	-0.0254	-0.0817	-0.032	0.0251	0.1054	-0.0205	0.0077	0.1218	-0.0094	0.1266	31.984	40.4432	92.9096
22	0.9283	-0.0345	0.3186	0.2976	-0.3013	1.4193	0.008	0.0976	0.006	-0.1394	-0.112	0.0011	0.1777	0.0925	0.1028	0.1526	-0.0003	0.0258	0.1135	0.0224	0.1233	39.2783	35.9301	71.2057
23	0.9165	0.3282	0.0684	0.8397	-0.3825	0.9835	-0.002	-0.0446	0.0108	-0.0815	-0.0031	-0.0593	0.1295	0.0025	-0.0094	0.1371	-0.0139	0.0141	0.1263	0.011	0.1223	35.9239	28.2996	76.494
24	0.6344	0.0572	-0.2738	0.569	-0.1283	0.7942	0.0597	-0.0723	0.0566	-0.0187	-0.07	-0.0232	0.0198	0.0784	0.0175	0.0982	-0.0176	0.0038	0.1239	0.0095	0.1296	40.8821	36.9688	84.583
25	0.969	0.1445	-0.2286	1.0517	0.8688	3.0074	0.0935	-0.1317	0.1396	-0.1386	-0.0791	-0.0525	-0.4548	0.0998	0.0108	0.1174	-0.0393	0.0039	0.1271	0.0181	0.1702	44.2589	50.136	89.358
26	0.5388	0.2216	-0.6641	0.535	-0.3396	1.1825	0.0202	0.0497	0.1282	-0.1054	0.0294	-0.0221	0.0507	-0.0586	-0.0418	0.162	-0.0051	0.0046	0.1636	0.0137	0.1533	31.0079	39.8264	69.8612
27	0.7558	0.2657	0.1883	3.725	0.2417	0.3552	0.0132	-0.1289	0.1238	0.0742	-0.1171	0.5663	-0.1544	-0.253	0.0952	0.1867	0.0079	0.0321	0.2557	-0.0167	0.2536	17.9909	43.317	84.475

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 70 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 151 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 152 through 234 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 235 through 256 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 257 through 291 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 292 through 320 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 321 through 352 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 70 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 71 through 150 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 151 through 256 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 257 through 290 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 291 through 320 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 321 through 348 )	B
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 28 through 70 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 71 through 151 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 152 through 234 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 235 through 291 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 292 through 321 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 322 through 343 )	C
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 28 through 70 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 71 through 151 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 152 through 167 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 168 through 207 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 208 through 256 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 257 through 291 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 292 through 320 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 321 through 339 )	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://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