PDB-3urm: Crystal structure of the periplasmic sugar binding protein ChvE

ID or keywords:

Entry

Database: PDB / ID: 3urm

Title

Crystal structure of the periplasmic sugar binding protein ChvE

Components

Multiple sugar-binding periplasmic receptor ChvE

Keywords

SUGAR BINDING PROTEIN / periplasmic binding protein / SUGAR-BINDING PROTEIN /

sugar /

periplasmic

Function / homology

Function and homology information

chemotaxis /

periplasmic space
Similarity search - Function

Biological species

Agrobacterium tumefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.801 Å

Authors

Hu, X. / Zhao, J. / Binns, A. / Degrado, W.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals.
Authors: Hu, X. / Zhao, J. / Degrado, W.F. / Binns, A.N.

History

Deposition	Nov 22, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3urm.cif.gz	277.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3urm.ent.gz	228.4 KB	Display	PDB format
PDBx/mmJSON format	3urm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ur/3urm ftp://data.pdbj.org/pub/pdb/validation_reports/ur/3urm	HTTPS FTP

-
Related structure data

Related structure data	3uugC 1drkS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4wwh-1 1usi-1 3uug-1 3lhs-d 1z2o-d 6spi-3 4ys6-d 4wwh-2 1dml-1 6ly2-2 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
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: Multiple sugar-binding periplasmic receptor ChvE

B: Multiple sugar-binding periplasmic receptor ChvE

hetero molecules

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

1

A: Multiple sugar-binding periplasmic receptor ChvE

hetero molecules

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

2

B: Multiple sugar-binding periplasmic receptor ChvE

hetero molecules

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

Unit cell

Length a, b, c (Å)	130.076, 130.076, 64.676
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein

Multiple sugar-binding periplasmic receptor ChvE

Mass: 35868.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4267, Atu2348, chvE / Plasmid: pJZ01 / Production host:

Escherichia coli (E. coli) / Strain (production host): E. coli BL21(DE3) / References: UniProt: P25548

#2: Sugar

ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose /

Galactose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#3: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.2 Å³/Da / Density % sol: 44.14 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 32% PEG4000, 0.2M Magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2010
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 54466 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / B_iso Wilson estimate: 32.8 Å² / R_sym value: 0.082 / Net I/σ(I): 34.55
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 952 / R_sym value: 0.494 / % possible all: 96.9

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6_289)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1drk

1drk

Resolution: 1.801→42.577 Å / SU ML: 0.21 / σ(F): 0.09 / σ(I): 0 / Phase error: 18.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1949	2689	5.09 %	random
R_work	0.1492	-	-	-
obs	0.1514	52840	91.47 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.818 Å² / k_sol: 0.314 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.4439 Å²	0 Å²	-0 Å²
2-	-	0.4439 Å²	0 Å²
3-	-	-	-0.8878 Å²

Refinement step

Cycle: LAST / Resolution: 1.801→42.577 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5024	0	24	659	5707

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5157
X-RAY DIFFRACTION	f_angle_d	0.891	6994
X-RAY DIFFRACTION	f_dihedral_angle_d	13.744	1894
X-RAY DIFFRACTION	f_chiral_restr	0.064	803
X-RAY DIFFRACTION	f_plane_restr	0.004	905

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8014-1.8657	0.231	234	0.1893	4526	X-RAY DIFFRACTION	83
1.8657-1.9404	0.2232	248	0.1756	4876	X-RAY DIFFRACTION	89
1.9404-2.0288	0.2285	270	0.165	4972	X-RAY DIFFRACTION	91
2.0288-2.1357	0.2253	276	0.1557	5128	X-RAY DIFFRACTION	94
2.1357-2.2695	0.2077	283	0.1517	5125	X-RAY DIFFRACTION	94
2.2695-2.4447	0.2037	283	0.1552	5116	X-RAY DIFFRACTION	94
2.4447-2.6907	0.2222	289	0.1586	5139	X-RAY DIFFRACTION	94
2.6907-3.08	0.2107	274	0.1621	5123	X-RAY DIFFRACTION	93
3.08-3.88	0.1694	263	0.1383	5102	X-RAY DIFFRACTION	93
3.88-42.5892	0.1645	269	0.1269	5044	X-RAY DIFFRACTION	90

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	1.0226	-0.3013	0.4212	1.6507	0.4651	2.2885	-0.2244	-0.1688	-0.0644	0.2555	0.021	-0.1451	0.1817	0.2157	0.0781	0.1232	0.0052	-0.0257	0.192	-0.0142	0.143	-41.2948	50.7998	5.5979
2	2.0085	-0.786	-1.7268	0.958	1.0416	4.4144	0.1097	-0.0564	0.4845	0.097	0.162	-0.1973	-0.4281	0.0034	-0.2364	0.1686	0.0193	-0.0039	0.1663	-0.0203	0.1964	-43.1275	57.5165	4.1971
3	1.0737	0.0164	0.6384	2.0169	0.1429	1.1933	0.0851	-0.0859	-0.1247	0.2046	0.0588	-0.4097	0.2446	0.2184	-0.1515	0.152	0.0334	-0.0294	0.1953	-0.0292	0.1764	-37.6785	43.0893	6.5018
4	1.6556	-0.0776	-0.3132	1.7861	-0.0202	0.1993	-0.1132	-0.1827	-0.0266	0.3052	0.1918	0.0121	0.1976	0.1649	-0.0722	0.1706	0.0561	0.003	0.1801	0.0105	0.1401	-44.8942	44.179	9.7864
5	2.0815	1.0902	-1.1867	2.2365	-0.7574	4.4101	-0.0252	-0.2688	-0.3485	0.2801	0.1455	-0.0401	0.9975	-0.1351	-0.1073	0.2542	-0.0329	-0.0455	0.1965	0.0618	0.2096	-48.9196	35.3275	9.7092
6	0.4981	-0.2556	0.0877	2.055	-0.855	1.2493	-0.0504	0.0405	0.024	0.0744	0.2327	0.3348	0.1686	-0.2992	-0.1585	0.1077	-0.0091	0.017	0.1806	0.0307	0.1624	-51.7133	42.1432	4.5553
7	0.2399	-0.1192	-0.8634	0.8526	0.218	1.9329	-0.0075	0.1169	-0.0075	-0.1589	0.1334	0.1676	-0.0304	-0.4615	-0.1221	0.1256	-0.0424	-0.0294	0.2297	0.0368	0.1438	-53.5045	50.5681	-15.8713
8	2.6055	-2.2001	-0.5694	4.0483	1.7279	5.0815	-0.1078	0.4907	0.4466	-0.9249	-0.5724	0.6245	-1.1293	-1.472	0.533	0.4534	-0.0188	-0.1711	0.5708	0.0036	0.2779	-55.3781	51.1944	-37.0903
9	0.3772	0.0092	-0.5058	0.527	-0.0717	1.1331	-0.1086	0.1647	-0.1231	-0.1959	0.1476	0.0692	0.3044	-0.436	-0.0208	0.2177	-0.1142	-0.0133	0.2311	0.0046	0.1404	-51.5229	41.6972	-22.9201
10	4.9832	3.6254	-3.6758	2.7186	-2.6853	6.5113	-0.8456	0.1379	-0.1839	-0.8297	0.6073	-0.0543	1.2289	0.6121	0.0279	0.4376	-0.1927	0.0072	0.2346	-0.0165	0.2121	-46.6442	34.6486	-28.3172
11	0.9947	0.1783	-0.9916	1.4266	0.5629	4.0832	-0.0977	0.0423	-0.127	-0.185	0.0509	-0.0993	0.6665	0.2911	0.0701	0.2757	-0.0197	0.0367	0.1925	-0.0399	0.1986	-38.5704	37.7648	-22.0213
12	1.0202	0.2821	0.4363	1.6589	-0.3278	0.2839	0.0056	0.3302	-0.0587	-0.2985	0.0579	-0.1312	0.1308	0.229	-0.0534	0.1928	-0.0575	0.035	0.2448	-0.0325	0.1208	-39.0007	45.8121	-26.022
13	1.4305	-0.2915	-1.3222	3.1091	1.4076	1.9658	0.0053	0.3472	0.2291	-0.7464	0.216	-0.3853	-0.7196	0.3935	-0.2472	0.3124	-0.1466	0.0662	0.316	-0.0564	0.1924	-34.6634	50.3107	-34.1987
14	0.6501	-0.4564	-0.1932	1.0213	-0.2218	1.5443	-0.0687	0.0552	0.0437	-0.1506	0.0728	-0.2322	0.1612	0.0524	-0.0189	0.1394	-0.036	0.017	0.1775	-0.0013	0.1696	-39.5839	56.0721	-20.1924
15	0.3267	0.0667	0.1375	0.4203	-0.1794	1.3356	-0.0341	0.0425	0.2193	0.0413	0.1309	-0.0223	-0.175	-0.2695	-0.0762	0.1405	0.0315	0.0065	0.1693	0.0095	0.2183	-50.701	57.4463	-0.3335
16	1.285	-0.4276	1.7128	2.8087	1.678	6.8291	-0.3088	-0.7922	0.2091	0.4105	0.0404	0.6282	-0.2038	-1.7398	-0.019	0.2576	0.0806	0.052	0.4836	0.0574	0.2379	-60.6196	53.2785	7.743
17	0.5085	0.9921	0.4394	4.8881	-1.1545	1.6249	-0.0202	-0.1463	0.0341	-0.3569	0.3764	0.8298	0.2038	-0.4066	-0.3128	0.1252	-0.0671	-0.0186	0.3264	0.1167	0.2528	-60.546	40.3257	-1.9757
18	0.534	0.1464	-0.1409	0.6791	-0.2555	0.0992	0.0793	-0.2336	0.2337	-0.0702	0.2292	0.2517	-0.0398	-0.0547	-0.2612	0.123	0.0023	-0.0053	0.2339	0.0617	0.1884	-54.3733	55.2855	-9.4828
19	1.0256	-0.0895	-0.502	0.2683	-0.5737	1.4707	-0.0152	0.0801	0.3673	-0.0541	-0.0367	-0.0493	-0.0005	-0.2107	0.074	0.1353	-0.0147	-0.0016	0.1545	0.0231	0.2538	-43.4266	66.0156	-15.7925
20	0.5893	-1.0069	-0.1972	1.9897	0.2407	0.1654	0.3295	0.4849	0.3463	-0.5379	-0.0559	-0.4081	-0.1414	0.0868	-0.1797	0.1643	-0.0557	0.0451	0.2741	0.0028	0.3411	-33.8187	67.7849	-13.5731
21	1.6826	-0.155	-0.8738	0.2539	0.141	0.4065	-0.1366	-0.2458	0.2326	0.1555	-0.0063	0.0228	0.2462	0.1279	0.0054	0.2003	0.0586	-0.0144	0.2995	-0.0534	0.2891	-56.4009	71.3373	-5.2456
22	0.2815	-0.2387	-0.1805	0.4579	0.6345	2.5687	-0.1288	0.0779	0.4584	-0.0883	0.1123	-0.333	-0.0401	0.5255	0.0129	0.147	0.0218	0.0018	0.245	-0.0379	0.3665	-51.7655	73.4469	-10.9308
23	2.0111	-2.5598	-0.1888	3.4816	0.6927	2.876	0.0293	-0.3809	-0.0212	0.4141	0.2637	-0.9446	0.2973	0.5674	-0.3516	0.2029	0.0094	-0.0372	0.4014	-0.0645	0.3117	-52.9245	70.9694	-2.5455
24	3.8053	-0.9746	-2.5939	0.7896	0.5033	2.0535	-0.1882	-0.5376	-0.1445	0.2541	-0.0092	0.134	0.1484	0.1334	0.099	0.232	0.0058	0.0472	0.2355	0.0237	0.2751	-66.5025	64.9759	-4.5963
25	0.9627	0.4536	0.0019	1.0882	0.5948	2.2319	0.0338	-0.6528	0.3943	0.027	0.0515	0.2508	0.0192	-0.0893	-0.0241	0.1405	0.042	0.0472	0.3449	-0.0956	0.2999	-66.4794	72.5199	-1.9793
26	0.6171	-2.0275	0.0951	7.4957	0.6856	6.9271	0.1135	-1.537	0.4461	0.7947	0.5107	0.1871	0.3114	0.0654	-0.3852	0.2278	0.0834	0.0909	0.7294	-0.2488	0.3685	-68.8548	77.1352	5.3828
27	0.3123	-0.5087	-0.2496	0.7975	0.737	2.9542	0.071	-0.063	0.5565	-0.1007	0.0775	-0.0232	-0.2865	-0.0855	-0.1015	0.161	-0.0003	0.0278	0.2334	-0.0138	0.4842	-64.6031	82.3518	-16.7466
28	2.279	-1.0285	3.0329	1.3083	-2.0831	9.6876	-0.1724	0.6584	1.106	-0.7817	0.2094	0.2325	-1.3941	0.0448	0.1653	0.6649	-0.0026	-0.0034	0.5897	0.2977	0.6376	-62.0635	86.9153	-44.8579
29	0.978	-0.6726	-0.015	1.5183	0.5073	1.3994	0.1004	0.1793	0.3301	-0.2933	-0.174	0.1726	-0.3794	-0.2411	0.0097	0.1703	0.0576	-0.0025	0.2508	0.0671	0.3777	-70.1984	79.5086	-29.8065
30	2.3309	-2.7373	0.5706	3.677	-0.4399	1.8402	0.2164	0.9867	0.4098	-0.7193	-0.2637	0.3973	-0.3837	-0.7165	-0.0537	0.4412	0.1973	-0.1057	0.491	0.1448	0.4108	-74.2439	80.8795	-41.5835
31	0.1694	-0.6333	0.4499	3.0493	-1.8316	6.6691	-0.0943	-0.3859	-0.0418	-0.1897	0.1405	0.3194	0.353	-0.8707	0.0265	0.1329	0.0025	0.0013	0.2979	0.0156	0.375	-72.4353	71.0609	-26.0844
32	1.616	-0.375	1.0172	2.0363	0.1791	0.7853	0.0271	0.1541	-0.0019	-0.3578	-0.1244	0.2892	-0.1305	0.0093	0.0897	0.1886	0.0211	-0.0108	0.2987	0.0171	0.2664	-66.7044	67.7801	-37.1295
33	7.0936	2.7708	-0.9438	8.2266	2.1048	1.2496	0.2597	1.9249	0.2061	-1.7601	-0.3456	-0.3775	-0.5516	-0.2082	0.0352	0.3505	0.0988	0.0646	0.5669	0.0678	0.2159	-59.118	67.3726	-46.3195
34	0.7597	0.0215	0.3337	0.3926	-0.0601	0.098	0	0.1322	0.406	-0.0471	0.0042	-0.1475	-0.2649	-0.1688	-0.046	0.1395	0.0046	0.0484	0.2921	0.0905	0.266	-53.7606	73.0817	-32.7372
35	1.3683	-0.2686	-0.0591	0.2756	-0.3578	0.4624	-0.0145	-0.3127	0.6885	0.1776	0.0053	-0.1457	-0.1826	0.2305	0.0059	0.1659	-0.0235	0.0442	0.3065	-0.0794	0.4687	-52.8972	82.041	-12.2229
36	1.0672	0.8198	0.3977	1.4035	1.549	2.6532	-0.1511	-0.4925	1.0354	0.5525	0.2013	0.026	-1.2957	0.7214	-0.2928	0.3614	-0.0279	0.0165	0.428	-0.2709	0.5966	-58.4096	90.2082	-2.0901
37	1.307	2.2031	-0.9409	3.9784	-1.4213	2.2272	0.4813	-0.4378	1.2362	0.3547	0.3262	1.8011	-0.2758	-0.3069	-0.7471	0.212	0.0467	0.0791	0.2251	0.0062	0.8457	-71.8898	87.7572	-11.6171
38	1.0083	-0.4839	-0.4945	0.7306	1.0819	3.1028	0.3302	-0.2744	1.0983	-0.1659	-0.0769	0.0707	-0.775	0.4595	-0.0954	0.2197	-0.0276	0.1071	0.227	-0.0584	0.6723	-61.314	87.4984	-14.8067
39	1.815	-1.861	0.6421	2.5204	-0.5147	1.3653	-0.0434	0.091	1.0591	0.0204	0.1499	-0.7772	-0.5662	0.2427	0.081	0.1397	-0.0848	0.1351	0.2275	0.1063	0.5615	-45.1911	79.2446	-28.4017
40	0.6174	-1.0289	-1.3089	6.0693	1.8741	3.8537	-0.2025	0.4988	0.304	-1.0405	0.5248	-1.8274	0.0309	0.4218	-0.3484	0.2293	-0.0485	0.089	0.3485	0.0008	0.5005	-40.3233	70.1024	-26.8817

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:16)
2	X-RAY DIFFRACTION	2	(chain A and resid 17:34)
3	X-RAY DIFFRACTION	3	(chain A and resid 35:54)
4	X-RAY DIFFRACTION	4	(chain A and resid 55:69)
5	X-RAY DIFFRACTION	5	(chain A and resid 70:82)
6	X-RAY DIFFRACTION	6	(chain A and resid 83:100)
7	X-RAY DIFFRACTION	7	(chain A and resid 101:124)
8	X-RAY DIFFRACTION	8	(chain A and resid 125:131)
9	X-RAY DIFFRACTION	9	(chain A and resid 132:168)
10	X-RAY DIFFRACTION	10	(chain A and resid 169:174)
11	X-RAY DIFFRACTION	11	(chain A and resid 175:200)
12	X-RAY DIFFRACTION	12	(chain A and resid 201:222)
13	X-RAY DIFFRACTION	13	(chain A and resid 223:237)
14	X-RAY DIFFRACTION	14	(chain A and resid 238:259)
15	X-RAY DIFFRACTION	15	(chain A and resid 260:277)
16	X-RAY DIFFRACTION	16	(chain A and resid 278:288)
17	X-RAY DIFFRACTION	17	(chain A and resid 289:299)
18	X-RAY DIFFRACTION	18	(chain A and resid 300:310)
19	X-RAY DIFFRACTION	19	(chain A and resid 311:324)
20	X-RAY DIFFRACTION	20	(chain A and resid 325:330)
21	X-RAY DIFFRACTION	21	(chain B and resid 2:15)
22	X-RAY DIFFRACTION	22	(chain B and resid 16:29)
23	X-RAY DIFFRACTION	23	(chain B and resid 30:42)
24	X-RAY DIFFRACTION	24	(chain B and resid 43:55)
25	X-RAY DIFFRACTION	25	(chain B and resid 56:76)
26	X-RAY DIFFRACTION	26	(chain B and resid 77:86)
27	X-RAY DIFFRACTION	27	(chain B and resid 87:120)
28	X-RAY DIFFRACTION	28	(chain B and resid 121:130)
29	X-RAY DIFFRACTION	29	(chain B and resid 131:159)
30	X-RAY DIFFRACTION	30	(chain B and resid 160:172)
31	X-RAY DIFFRACTION	31	(chain B and resid 173:184)
32	X-RAY DIFFRACTION	32	(chain B and resid 185:222)
33	X-RAY DIFFRACTION	33	(chain B and resid 223:236)
34	X-RAY DIFFRACTION	34	(chain B and resid 237:258)
35	X-RAY DIFFRACTION	35	(chain B and resid 259:277)
36	X-RAY DIFFRACTION	36	(chain B and resid 278:288)
37	X-RAY DIFFRACTION	37	(chain B and resid 289:296)
38	X-RAY DIFFRACTION	38	(chain B and resid 297:308)
39	X-RAY DIFFRACTION	39	(chain B and resid 309:324)
40	X-RAY DIFFRACTION	40	(chain B and resid 325:330)

-
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