PDB-4pgn: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR...

ID or keywords:

Entry

Database: PDB / ID: 4pgn

Title

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634, TARGET EFI-510120) WITH BOUND INDOLE PYRUVATE

Components

Extracellular solute-binding protein, family 7

Keywords

TRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

transmembrane transport / periplasmic space
Similarity search - Function

Biological species

Desulfovibrio desulfuricans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.8 Å

Authors

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

Funding support

United States, 1items

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	May 2, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 28, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 2015	Group: Derived calculations
Revision 1.2	Feb 25, 2015	Group: Database references
Revision 1.3	Oct 14, 2015	Group: Data collection
Revision 1.4	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Refinement description Category: pdbx_audit_support / pdbx_struct_oper_list / software Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Dec 27, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4pgn.cif.gz	713.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4pgn.ent.gz	603.1 KB	Display	PDB format
PDBx/mmJSON format	4pgn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4pgn_validation.pdf.gz	484.3 KB	Display	wwPDB validaton report
Full document	4pgn_full_validation.pdf.gz	488.6 KB	Display
Data in XML	4pgn_validation.xml.gz	56.9 KB	Display
Data in CIF	4pgn_validation.cif.gz	85.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pg/4pgn ftp://data.pdbj.org/pub/pdb/validation_reports/pg/4pgn	HTTPS FTP

-
Related structure data

Related structure data	4ln5C 4mcoC 4mevC 4mhfC 4mijC 4mncC 4mniC 4mx6C 4n15C 4n17C 4n4uC 4n6dC 4n6kC 4n8gC 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 4pgpC 4uabC C: citing same article (ref.)
Similar structure data	3npr-d 4nap-4 2zcq-d 4ea1-d 6n4l-d 3vjd-d 7ai1-3 3w7f-2 5hjq-d 5ycp-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-510102

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Extracellular solute-binding protein, family 7

B: Extracellular solute-binding protein, family 7

C: Extracellular solute-binding protein, family 7

D: Extracellular solute-binding protein, family 7

hetero molecules

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

1

A: Extracellular solute-binding protein, family 7

hetero molecules

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

2

B: Extracellular solute-binding protein, family 7

hetero molecules

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

3

C: Extracellular solute-binding protein, family 7

hetero molecules

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

4

D: Extracellular solute-binding protein, family 7

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.122, 144.459, 95.466
Angle α, β, γ (deg.)	90.000, 90.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

biological unit is a monomer

#1: Protein	Extracellular solute-binding protein, family 7 / TRAP PERIPLASMIC SOLUTE BINDING PROTEIN Mass: 36869.078 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Strain: G20 / Gene: Dde_0634 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q315G1
#2: Chemical	ChemComp-3IO / 3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID Mass: 203.194 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₉NO₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1249 / 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: 2.34 Å³/Da / Density % sol: 47.51 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein (68.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT), Reservoir (0.2 M di-Ammonium Hydrogen Citrate pH 5.0, 20 %(w/v) PEG 3350), Cryoprotection (80% Reservoir + 20% Ethylene Glycol

-
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: Mar 21, 2014 / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.8→33.9 Å / Num. obs: 124994 / % possible obs: 99.8 % / Redundancy: 3.8 % / B_iso Wilson estimate: 18.15 Å² / R_merge(I) obs: 0.111 / R_pim(I) all: 0.066 / Net I/σ(I): 7.2 / Num. measured all: 470607 / Scaling rejects: 2

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	% possible all
1.8-1.83	3.7	0.8	1.7	22860	6132	0.48	99.9
9.86-33.9	3.4	0.035	15.7	2181	642	0.022	81.4

-
Processing

Software

Name	Version	Classification
Aimless	0.1.27	data scaling
PDB_EXTRACT	3.14	data extraction
PHENIX	(phenix.refine: 1.8.1_1168)	refinement

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.8→29.301 Å / FOM work R set: 0.8502 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1959	6275	5.03 %	Random Selection
R_work	0.1568	118551	-	-
obs	0.1589	124826	99.71 %	-

Solvent computation

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

Displacement parameters

B_iso max: 104.44 Å² / B_iso mean: 27.28 Å² / B_iso min: 8.17 Å²

Refinement step

Cycle: final / Resolution: 1.8→29.301 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9509	0	134	1249	10892
B_iso mean	-	-	20.66	37.21	-
Num. residues	-	-	-	-	1237

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	9826
X-RAY DIFFRACTION	f_angle_d	1.29	13356
X-RAY DIFFRACTION	f_chiral_restr	0.075	1482
X-RAY DIFFRACTION	f_plane_restr	0.007	1737
X-RAY DIFFRACTION	f_dihedral_angle_d	13.63	3599

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 (%)
1.8-1.8205	0.3089	210	0.2621	3867	4077	100
1.8205-1.8419	0.2751	224	0.2476	3963	4187	100
1.8419-1.8643	0.261	240	0.233	3922	4162	100
1.8643-1.8879	0.2997	183	0.2311	3935	4118	100
1.8879-1.9128	0.2582	183	0.2194	3995	4178	100
1.9128-1.939	0.2449	217	0.2094	3930	4147	100
1.939-1.9667	0.2594	213	0.2065	3917	4130	100
1.9667-1.996	0.245	201	0.2053	3992	4193	100
1.996-2.0272	0.2577	188	0.1891	3976	4164	100
2.0272-2.0604	0.2273	223	0.1873	3895	4118	100
2.0604-2.0959	0.2462	218	0.1763	3998	4216	100
2.0959-2.134	0.2143	192	0.1663	3893	4085	100
2.134-2.1751	0.2189	212	0.1602	4009	4221	100
2.1751-2.2195	0.1851	193	0.1461	3974	4167	100
2.2195-2.2677	0.2091	201	0.1455	3961	4162	100
2.2677-2.3204	0.1889	210	0.1412	3937	4147	100
2.3204-2.3784	0.1817	199	0.1351	4001	4200	100
2.3784-2.4427	0.172	200	0.1335	3951	4151	100
2.4427-2.5145	0.198	200	0.1339	3991	4191	100
2.5145-2.5957	0.1912	233	0.1385	3895	4128	100
2.5957-2.6884	0.1982	247	0.1455	3935	4182	100
2.6884-2.7959	0.1893	180	0.1421	3998	4178	100
2.7959-2.9231	0.1933	208	0.1488	3976	4184	100
2.9231-3.077	0.2132	203	0.1526	3978	4181	100
3.077-3.2696	0.1954	222	0.1541	3948	4170	100
3.2696-3.5216	0.186	183	0.1405	3995	4178	100
3.5216-3.8753	0.1496	241	0.135	3964	4205	100
3.8753-4.4344	0.1536	222	0.1228	3942	4164	100
4.4344-5.5806	0.1487	217	0.1364	3995	4212	100
5.5806-29.3047	0.2016	212	0.1864	3818	4030	95

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	0.7471	0.4904	0.1178	1.6254	-0.4951	0.9313	-0.0762	0.1191	0.2383	0.0678	0.1336	0.2719	-0.2034	-0.061	-0.0404	0.16	0.0038	0.0143	0.1417	0.0521	0.1904	18.5868	15.2474	52.4146
2	1.9593	-0.4727	-0.2038	1.3876	-0.0791	0.8085	-0.063	0.1193	0.0263	0.1835	0.1714	0.64	-0.1347	-0.1686	-0.0729	0.1455	0.0274	0.0666	0.1674	0.0851	0.2948	13.5315	9.7975	54.9455
3	1.7152	-0.191	-0.3435	1.1277	-0.4236	1.4512	0.0278	-0.1139	-0.0873	0.236	-0.012	-0.1968	-0.1041	0.1025	-0.018	0.1494	-0.0126	-0.0378	0.1532	-0.0063	0.1412	33.2439	-0.2933	65.2516
4	2.2185	-0.4865	0.1376	1.0289	-0.4077	0.799	-0.0049	0.1289	-0.0588	-0.0256	-0.0341	-0.1982	-0.0105	0.1231	0.0329	0.1072	-0.0059	0.0022	0.1767	-0.0079	0.1263	34.4031	1.8717	54.9639
5	1.2292	0.1004	0.4512	1.8913	-0.7588	1.4749	-0.0493	0.4079	0.2406	-0.2209	0.1086	0.2805	-0.1112	-0.0552	0.0043	0.1446	-0.0376	-0.0241	0.19	0.0903	0.1735	20.8745	12.7695	46.2523
6	2.9935	0.7922	-1.3548	0.5234	-0.8596	1.3627	0.0346	0.4333	-0.6007	-0.0317	0.05	-0.2455	0.2969	-0.1284	-0.1387	0.2265	-0.0202	0.0041	0.1878	-0.0423	0.3386	31.1051	-13.2908	58.2894
7	2.4589	-0.1397	0.1342	1.7767	-0.2918	1.1574	0.0267	-0.0912	-0.0711	0.0799	0.1086	0.2338	-0.04	-0.0907	-0.1176	0.1343	-0.038	0.0316	0.1785	0.0062	0.1558	8.1991	-3.8562	59.3791
8	1.0514	0.3205	0.0868	1.4429	0.3926	1.5202	-0.0358	-0.1327	0.136	-0.0075	0.0283	-0.1041	-0.1812	0.0132	0.0023	0.1468	0.0303	0.001	0.1237	-0.0433	0.1499	28.1154	40.1082	96.6689
9	0.8973	0.0524	0.0454	1.4704	0.4628	0.5353	-0.055	0.0508	0.0057	-0.1701	0.0788	-0.2579	-0.0721	0.0445	-0.0258	0.1396	-0.0131	0.0383	0.1178	-0.029	0.1162	33.1149	27.5224	86.1452
10	1.9167	0.4885	-0.0857	1.4679	0.3202	0.7681	-0.0824	0.1338	0.0429	-0.1495	0.194	-0.3359	-0.0946	0.0869	-0.0712	0.1225	-0.0274	0.0426	0.1361	-0.031	0.1819	35.7878	27.2694	88.2313
11	1.957	0.6036	0.1692	1.3074	0.3492	1.5068	-0.0604	0.047	-0.213	-0.2575	0.0158	0.1938	-0.0577	-0.1305	0.0351	0.134	-0.0053	-0.0078	0.1178	-0.0162	0.1659	15.8961	17.0849	78.4321
12	1.8383	0.6238	0.0539	1.0737	0.3194	0.7771	-0.0946	-0.1424	-0.0405	-0.0146	0.0898	0.2734	-0.0156	-0.1361	-0.002	0.1058	-0.0025	0.0148	0.1635	0.018	0.1686	14.8581	19.6101	88.6386
13	1.609	0.3949	0.4203	1.8472	0.3434	1.3919	-0.0446	-0.1864	0.0556	0.176	0.0533	-0.1441	-0.1252	-0.0924	0.0236	0.1114	0.0264	0.0095	0.1223	-0.0372	0.1105	29.3628	30.8891	96.8522
14	1.447	0.0238	-0.5059	0.0667	-0.1593	1.3221	-0.0401	-0.2535	-0.1977	-0.1823	0.2322	0.4558	0.4924	-0.107	0.3645	0.0961	-0.0767	0.0576	0.1897	0.0808	0.4416	16.962	5.4997	85.732
15	0.9748	0.4081	0.3869	1.4154	0.5185	1.2249	0.0034	0.0066	-0.1434	-0.0863	0.2135	-0.3429	-0.088	0.2027	-0.1576	0.134	-0.0088	0.0519	0.1515	-0.0357	0.2021	41.0283	13.391	84.345
16	1.9691	0.2327	0.4179	1.1941	-0.1067	1.2453	-0.0683	0.1593	-0.0235	-0.1152	0.149	0.1791	0.0855	-0.028	-0.0898	0.2308	-0.0174	-0.013	0.1846	0.1124	0.266	29.1136	31.3985	41.3527
17	0.7168	0.3725	0.6846	1.329	-0.2241	2.6001	-0.0154	0.2796	-0.5854	-0.2193	0.2	-0.3466	0.2342	0.385	-0.083	0.2541	0.027	0.0106	0.2601	0.0173	0.2798	43.4404	28.1915	37.9939
18	1.3276	0.366	0.4372	1.4428	-0.2962	0.9813	-0.2627	0.3479	0.4757	-0.1237	0.1709	0.1111	-0.0769	0.3736	0.1185	0.1982	-0.0548	-0.066	0.2725	0.1646	0.2982	41.7661	46.0539	39.4307
19	1.4576	0.1122	0.3656	1.0418	-0.0493	1.307	-0.0246	-0.3652	0.0236	0.516	-0.0385	-0.0776	0.1189	0.1892	0.038	0.3521	0.0175	-0.0695	0.3744	0.0713	0.2138	48.707	43.2141	59.3345
20	2.0875	0.6746	0.2454	1.711	0.0871	1.7159	-0.144	0.0803	0.2738	-0.0647	0.1323	0.4466	0.0687	0.0256	-0.0083	0.2005	-0.018	-0.0244	0.1846	0.1397	0.2957	31.3212	39.7824	43.0772
21	0.9494	-0.2106	-0.3759	1.0864	-0.5301	2.4842	-0.2781	0.0835	0.4961	0.4021	0.0032	-0.1571	-0.2569	0.047	0.1792	0.355	-0.1127	-0.1204	0.392	0.0694	0.3878	51.4952	56.2588	52.6724
22	2.5864	-0.3695	-0.4876	1.3557	0.2435	1.3863	-0.358	0.0352	0.1657	0.0276	0.066	-0.0075	-0.128	0.2696	0.0255	0.2393	-0.0803	-0.1044	0.3503	0.1986	0.4525	42.5248	58.2755	36.5778
23	1.6069	0.1929	0.1577	1.3631	-0.1839	0.9726	0.0073	0.0599	-0.0692	-0.0409	0.0636	0.1145	0.0648	0.0235	-0.0547	0.1383	0.0123	0.002	0.0872	0.0578	0.1191	28.5118	-23.1415	89.5902
24	0.7342	0.1432	1.1448	1.5182	-0.128	2.8469	0.1291	0.0517	-0.2908	-0.1633	0.0369	-0.4047	0.3093	0.2507	-0.086	0.1706	0.0297	0.0348	0.1428	0.018	0.2186	42.9351	-26.2967	86.0892
25	0.6803	0.483	0.1759	1.2906	-0.165	0.9277	-0.0354	0.0367	0.0997	0.061	-0.028	-0.0721	-0.0535	0.169	0.0503	0.1305	-0.0057	0.0042	0.1473	0.0406	0.1324	41.8126	-7.1509	88.9442
26	0.995	0.3917	0.5874	1.1265	0.177	1.6659	-0.0017	0.1021	-0.0431	-0.1351	0.0791	-0.1452	-0.1178	0.0606	-0.0198	0.1239	-0.0027	0.0272	0.1067	0.0315	0.1034	40.323	-11.4524	85.7844
27	1	0.1239	-0.1364	0.3839	-0.2017	1.9194	-0.0554	-0.196	0.1876	0.438	-0.0597	-0.3105	-0.2662	0.2741	0.0508	0.3751	-0.0328	-0.1355	0.326	0.0165	0.1902	52.4158	-7.2289	108.8038
28	1.8638	-0.1439	0.2832	0.5653	-0.0746	1.6385	0.0537	-0.0323	-0.1083	0.2108	-0.1204	-0.1647	0.2007	0.3665	0.0216	0.3026	0.0273	-0.0906	0.2941	0.0622	0.1867	50.3358	-16.8586	106.282
29	1.0198	0.2182	0.1583	0.4633	-0.157	1.7312	-0.0302	-0.2056	-0.0203	0.395	0.093	-0.1075	-0.0304	0.1006	0.0147	0.308	0.0301	-0.0277	0.2092	0.0547	0.1067	40.9382	-11.6704	108.2359
30	1.758	0.645	1.4443	1.584	0.7936	2.2612	0.0443	0.1978	-0.144	-0.3212	0.0742	-0.0068	0.1183	0.0246	-0.0716	0.2223	0.0105	-0.0079	0.1283	0.0192	0.1117	35.135	-21.1694	78.0605
31	1.1279	0.1112	0.3954	1.2757	-0.2068	2.0807	0.0504	-0.2225	0.1835	0.1427	0.0697	0.2552	0.0866	-0.3124	-0.0841	0.1525	0.0108	0.0383	0.1424	0.07	0.1348	28.7748	-12.1125	97.3202
32	1.3541	-0.2213	-0.2181	0.519	-0.0917	0.0883	-0.1895	-0.0678	0.4256	0.3519	0.2908	-0.4799	-0.2938	-0.0417	-0.0169	0.6569	-0.1127	-0.0524	0.352	-0.0771	0.3426	48.0416	1.8797	110.4467
33	2.8623	0.6402	0.5377	1.0559	-0.3057	5.0678	-0.0729	0.02	-0.2125	0.2762	-0.2451	-0.6137	-0.093	0.3678	0.0975	0.1497	-0.0775	-0.0365	0.2099	0.0538	0.3201	55.1597	-0.8337	87.3462
34	3.3069	-0.5024	-0.6494	1.2869	0.1933	0.9	0.1332	0.0475	0.2319	0.0092	0.0128	0.037	-0.1029	-0.0248	-0.0598	0.1363	-0.0024	0.0227	0.1654	0.0104	0.2268	41.294	4.1576	85.3113

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 134 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 135 through 154 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 155 through 212 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 213 through 237 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 238 through 288 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 289 through 307 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 308 through 339 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 31 through 74 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 75 through 134 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 135 through 154 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 155 through 212 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 213 through 237 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 238 through 287 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 288 through 307 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 308 through 339 )	B
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 32 through 74 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 75 through 93 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 94 through 154 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 155 through 237 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 238 through 288 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 289 through 320 )	C
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 321 through 341 )	C
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 32 through 74 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 75 through 93 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 94 through 134 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 135 through 154 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 155 through 184 )	D
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 185 through 212 )	D
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 213 through 237 )	D
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 238 through 251 )	D
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 252 through 288 )	D
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 289 through 307 )	D
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 308 through 321 )	D
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 322 through 341 )	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

-
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