PDB-6hrc: Outward-facing PglK with ATPgammaS bound

ID or keywords:

Entry

Database: PDB / ID: 6hrc

Title

Outward-facing PglK with ATPgammaS bound

Components

WlaB protein

Keywords

TRANSPORT PROTEIN / ABC transporter

Function / homology

Function and homology information

ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
Similarity search - Function

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.3 Å

Authors

Perez, C. / Locher, K.P.

Funding support

Switzerland, 1items

Citation

Journal: Structure / Year: 2019
Title: Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation.
Authors: Perez, C. / Mehdipour, A.R. / Hummer, G. / Locher, K.P.

History

Deposition	Sep 26, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2019	Group: Data collection / Database references / Category: citation / pdbx_database_proc Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6hrc.cif.gz	942.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6hrc.ent.gz	797.7 KB	Display	PDB format
PDBx/mmJSON format	6hrc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6hrc_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	6hrc_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6hrc_validation.xml.gz	86 KB	Display
Data in CIF	6hrc_validation.cif.gz	113.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/6hrc ftp://data.pdbj.org/pub/pdb/validation_reports/hr/6hrc	HTTPS FTP

-
Related structure data

Related structure data	5c78S 5c73 5c76 5nbd S: Starting model for refinement
Similar structure data	5c73-1 6a6m-1 5c73-2 5vj1-2 5c73-3 6vqt-d 6pan-d 5vit-1 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	#123 - Mar 2010 P-glycoprotein similarity (10) #95 - Nov 2007 Multidrug Resistance Transporters similarity (10) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: WlaB protein

B: WlaB protein

C: WlaB protein

D: WlaB protein

hetero molecules

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

1

A: WlaB protein

B: WlaB protein

hetero molecules

defined by author&software
Evidence: gel filtration
130 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: WlaB protein

D: WlaB protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	125.680, 145.980, 206.760
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	WlaB protein Mass: 64559.621 Da / Num. of mol.: 4 / Mutation: E510Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O86150
#2: Chemical	ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.67 Å³/Da / Density % sol: 66.51 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: Na3Citrate: NaCl:MgCl2:ATPgammaS:PEG400

-
Data collection

Diffraction

Mean temperature: 293 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2016

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.3→19.995 Å / Num. obs: 52311 / % possible obs: 90.83 % / Redundancy: 13.8 % / R_rim(I) all: 0.181 / Net I/σ(I): 1.34

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
3.3-3.38	13.151	1.977	1.6	1110	0.459	2.057	24.7
3.38-3.48	13.411	2.197	1.44	2165	0.436	2.283	49.5
3.48-3.58	12.378	2.285	1.31	4048	0.404	2.384	95.2
3.58-3.7	13.737	1.713	1.92	4121	0.601	1.778	99.9
3.7-3.83	14.226	1.198	2.91	4013	0.8	1.242	100
3.83-3.97	14.086	0.984	3.52	3843	0.854	1.021	100
3.97-4.14	13.93	0.721	4.68	3714	0.901	0.748	100
4.14-4.32	13.736	0.505	6.33	3580	0.942	0.524	100
4.32-4.53	13.305	0.355	8.64	3409	0.968	0.369	100
4.53-4.78	12.194	0.248	11.13	3261	0.98	0.259	99.7
4.78-5.07	14.161	0.232	13.06	3110	0.988	0.241	100
5.07-5.42	14.073	0.219	13.39	2912	0.988	0.227	100
5.42-5.85	13.835	0.234	12.51	2727	0.987	0.243	100
5.85-6.41	13.311	0.192	14.56	2510	0.99	0.2	100
6.41-7.16	11.921	0.131	18.74	2272	0.994	0.137	99.7
7.16-8.27	13.717	0.073	32.06	2047	0.999	0.076	100
8.27-10.13	13.081	0.043	46.94	1736	0.999	0.045	100
10.13-14.33	11.471	0.037	50.66	1357	0.999	0.039	99.2
14.33-24.952	12.294	0.032	57.81	708	0.999	0.033	87.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5C78

5c78

Resolution: 3.3→19.995 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.53

	R_factor	Num. reflection	% reflection
R_free	0.2838	2665	5.09 %
R_work	0.2323	-	-
obs	0.2349	52311	90.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 602.5 Å² / B_iso mean: 143.8265 Å² / B_iso min: 34.3 Å²

Refinement step

Cycle: final / Resolution: 3.3→19.995 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18220	0	126	136	18482
B_iso mean	-	-	111.82	39.29	-
Num. residues	-	-	-	-	2256

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 19

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.3002-3.3599	0.467	36	0.3973	670	706	24
3.3599-3.4242	0.4009	63	0.3682	1103	1166	39
3.4242-3.4938	0.4148	95	0.36	1811	1906	63
3.4938-3.5693	0.3771	137	0.3584	2815	2952	99
3.5693-3.6519	0.3997	164	0.3442	2819	2983	100
3.6519-3.7426	0.4034	158	0.3079	2833	2991	100
3.7426-3.8431	0.3634	141	0.2918	2878	3019	100
3.8431-3.9554	0.316	144	0.2872	2852	2996	100
3.9554-4.082	0.3297	170	0.2765	2842	3012	100
4.082-4.2266	0.314	156	0.2563	2848	3004	100
4.2266-4.3941	0.2539	151	0.227	2877	3028	100
4.3941-4.5918	0.2727	144	0.2113	2877	3021	100
4.5918-4.8306	0.255	150	0.1922	2865	3015	100
4.8306-5.1285	0.2568	160	0.1981	2859	3019	100
5.1285-5.5167	0.2636	148	0.206	2914	3062	100
5.5167-6.0579	0.2868	157	0.2274	2905	3062	100
6.0579-6.9027	0.3138	161	0.238	2913	3074	100
6.9027-8.5807	0.2875	165	0.2112	2937	3102	100
8.5807-19.9958	0.2028	165	0.1804	3028	3193	100

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	5.6874	2.0667	-1.7421	2.937	-1.9252	2.8157	0.6412	-0.8637	1.6167	0.5689	-0.8802	-0.344	-1.9739	0.9591	0.0077	2.2461	-0.7038	0.2581	1.62	-0.4886	1.8256	25.998	17.2288	19.4419
2	2.1066	2.5068	-1.6497	2.5871	-2.2891	3.9099	0.7966	-0.9252	0.3502	0.7476	-0.7442	-0.4199	-1.3918	1.5956	-0.0879	1.1787	-0.3668	0.1737	1.5805	-0.4536	1.1078	19.3384	0.6311	21.1655
3	3.7027	0.0851	0.7868	3.4455	-0.8405	3.4898	0.4087	-1.2469	1.1809	0.9922	-0.5071	-0.1752	-1.1095	0.9506	0.069	0.9854	-0.1984	0.201	1.0901	-0.4393	0.875	2.2011	-0.8396	28.2419
4	1.8217	1.4738	-0.0219	5.2609	0.3621	0.0241	-0.2986	-0.4802	1.3329	0.6811	0.4199	-0.1323	-0.1642	0.2382	-0.0668	1.0527	0.1117	-0.1273	0.8585	-0.4088	1.5188	-8.5542	2.2809	19.9283
5	7.4898	4.5631	-1.705	9.3286	-3.6376	4.0663	-0.6979	1.1998	1.8064	-1.1269	0.8861	0.7243	-1.3497	1.5243	-0.1603	1.6643	-0.4991	-0.0536	1.3009	0.029	0.7836	-6.004	10.834	10.5162
6	5.7216	-1.7904	2.8222	0.7367	0.0635	4.043	-0.8698	1.3985	4.4815	-0.6181	0.5716	-1.0226	-1.7536	2.3593	0.4093	2.3273	-2.1721	0.5072	-0.5601	-1.9208	3.7823	9.2648	24.1171	12.8448
7	4.2763	0.0793	1.8371	2.6977	-1.3446	1.8011	-0.7796	-2.1961	0.3077	0.2805	0.8182	0.1035	0.5264	-1.0229	0.036	1.3568	0.0812	0.3204	2.182	-0.0584	0.6683	-11.0857	-25.0534	48.8673
8	2.5347	-0.1621	-1.2778	4.387	1.1592	8.0566	-0.4267	-1.3567	-0.3212	0.7309	0.4657	0.1	0.6909	0.628	-0.0943	0.6593	0.0956	-0.0431	1.3843	0.276	0.6709	-5.4313	-39.1511	37.5816
9	1.9321	-0.3539	2.7038	7.9006	-0.3914	4.3178	-0.0094	-2.3376	-2.0267	0.6023	0.0394	2.308	1.4985	0.1913	-0.0143	1.6744	0.1428	0.4995	1.8226	0.8879	1.1648	-16.8397	-46.2864	48.1152
10	2.9547	-0.1449	1.2919	6.2501	-2.9269	1.8198	0.2895	0.6997	0.767	-0.4181	0.1192	0.6621	0.4552	0.2486	-0.4525	1.8082	-0.0316	0.403	0.9946	-0.0577	0.6272	-3.3532	0.0631	-4.7771
11	6.0836	1.2951	2.5952	4.1594	-5.2386	9.7032	-0.062	3.5378	1.0462	-0.017	0.1385	-0.7912	-3.0335	2.2634	0.2331	2.7887	-0.8178	0.7565	2.3673	0.2881	2.6278	10.4168	35.0364	-12.18
12	1.0514	0.2715	-0.8009	4.4819	-2.7204	3.7976	0.419	0.14	1.0911	-0.152	-0.4768	-0.6785	-0.4978	0.8813	0.1111	0.7333	-0.1562	0.2609	0.658	0.018	1.0865	-6.1367	-2.2271	6.0968
13	4.8377	3.1267	-4.6308	6.6071	-5.386	7.0344	-0.0917	-0.153	0.4978	-0.5713	0.0608	-0.7675	-0.1512	0.3768	0.0432	0.7484	-0.173	0.1245	0.9473	-0.2887	0.8129	10.0019	-8.4918	8.7027
14	6.3494	0.0386	-2.4071	4.1139	-0.4153	7.7695	0.1693	-0.6809	1.3425	-0.7118	-0.0029	-1.2337	-0.6999	0.7628	0.2896	0.7369	-0.0742	-0.0382	1.0326	-0.2763	1.242	18.0466	-3.2056	13.6425
15	6.1777	2.6416	4.5735	6.3426	0.668	3.7467	-0.7759	-0.2516	1.9226	0.0755	-0.2691	1.7205	-2.5827	2.1602	0.8232	1.7508	-0.5303	0.33	1.4226	-0.1887	1.8489	20.4894	10.9126	-1.9365
16	7.2369	2.9305	-2.0218	2.6976	-2.7779	3.0043	0.2381	0.3468	-0.9898	0.2435	-0.3586	-0.4151	0.5494	0.0374	0.1812	0.7767	0.0421	0.0557	0.4583	-0.1448	0.9726	-22.1358	-38.8313	8.6645
17	3.8423	2.5542	2.4925	6.9581	1.5322	4.0666	0.219	-1.5958	-0.1545	0.8764	0.0312	0.4975	-0.0984	-0.7865	-0.1165	0.682	0.0327	0.316	1.3219	0.2282	0.781	-30.5744	-28.4244	30.3916
18	6.8683	-2.1957	2.3308	8.8857	-0.454	2.9369	0.9375	-2.1053	-2.1821	1.2448	-0.704	1.5876	0.8718	-1.4004	-0.3098	1.0265	-0.2572	0.3496	1.4149	0.2838	1.6926	-32.3465	-48.3003	24.0288
19	1.398	-2.1432	-1.0937	5.3923	3.9492	3.0735	0.4933	-1.0423	0.6579	0.6881	0.108	0.0553	-3.1926	0.3152	-0.2943	1.5802	-0.3114	-0.3221	1.2337	-0.1678	0.9597	27.6307	-31.9216	36.4718
20	0.8734	-0.8046	-0.0416	3.4979	0.3464	0.9146	-0.6709	0.6561	1.129	-0.1447	0.0444	-0.8721	-0.4643	1.0553	-0.0134	4.3337	-0.2698	-2.1738	3.2552	-1.1894	2.2534	41.0671	-25.5866	72.2686
21	2.9714	1.088	2.1245	1.5661	1.6251	7.9068	-0.9319	-2.0837	1.7621	0.5793	-1.5941	0.8748	-0.0958	0.1554	1.913	1.071	-0.0928	-0.1133	1.8711	-0.1484	0.8583	25.1141	-39.7667	44.4576
22	1.3339	0.1499	0.7368	3.8112	0.4547	3.8606	-1.0263	-0.9182	1.251	0.4964	0.3306	-0.4176	-1.3613	1.1407	0.3737	0.9641	-0.053	-0.4836	1.3616	-0.3727	1.2461	30.5825	-41.2388	26.5968
23	6.382	3.4535	1.3936	6.7409	4.5907	4.5801	-0.4374	-0.9327	1.6467	0.2191	0.285	0.7293	-0.3787	0.9845	0.0877	0.7513	-0.1029	-0.2653	0.8591	-0.1114	1.1418	41.6281	-49.4669	24.3668
24	9.2399	5.125	3.8079	7.1121	3.9099	7.3584	0.1732	-1.3544	-0.16	1.0484	0.1694	-0.8467	0.1918	1.8126	-0.7245	1.002	0.0163	-0.3044	1.3804	0.002	1.1184	50.0805	-50.0949	34.1276
25	1.9947	0.1826	-1.1613	0.2604	-0.5594	1.5277	-0.2631	-1.4849	0.9647	1.2876	0.3812	-0.7642	0.1188	1.3234	-0.057	1.4327	0.3211	-0.7388	1.8035	-0.4	1.6886	50.9626	-34.9477	47.5466
26	6.5812	1.3294	3.6451	4.1279	3.5377	5.0081	0.1496	0.7892	0.5044	-0.3526	0.4258	0.2852	0.1239	0.4108	-0.5861	0.6799	-0.1161	-0.114	0.8944	0.2381	0.7998	11.6519	-45.7421	-1.8007
27	5.7509	0.1756	-0.0038	7.4212	-1.7259	5.4297	0.1491	0.508	-0.6895	0.0804	0.2329	1.0093	0.4794	-0.5551	-0.3011	0.545	-0.2343	-0.056	0.6854	0.059	0.8342	2.0021	-60.3514	5.5545
28	7.597	4.6727	-5.5455	8.514	-3.3302	8.7154	0.6293	2.06	-2.3554	0.0346	-0.4961	0.2704	-0.003	-1.7003	-0.2122	0.5986	-0.1029	-0.2587	1.429	-0.1074	1.1106	-1.0513	-61.1001	-11.2947
29	2.9268	-0.8431	0.5561	2.5843	-2.1229	0.9747	0.9772	-2.118	-0.7834	2.2008	-0.1254	-2.12	1.0206	-0.0354	-0.7402	1.7029	0.2763	-0.7549	2.0006	-0.0767	1.5593	55.2396	-56.4134	48.8061
30	3.3772	-0.8639	1.5111	1.1974	-0.365	4.8592	-0.1407	-1.9723	-0.6152	0.6298	0.5918	-0.2119	0.468	-0.2387	-0.4577	1.0088	0.1099	-0.1336	1.6378	0.3474	0.7977	27.3524	-61.0046	36.9433
31	3.1415	-1.4116	0.7525	1.9323	-1.7186	8.0278	-0.2985	-1.5834	0.2838	0.7713	-0.2189	-0.6457	-0.9018	2.4647	0.2682	1.4625	-0.1374	-0.4197	2.3313	0.1569	0.9271	32.6857	-48.8142	54.2835
32	1.7238	-1.0139	0.1902	0.3841	0.2541	3.6704	-0.331	-0.3454	-1.2317	0.0196	0.1856	0.8327	1.0694	0.096	0.2422	1.4305	-0.0743	-0.0098	0.594	0.1783	1.8111	21.7876	-86.7819	9.8818
33	6.5785	-0.2445	-0.2038	4.8585	2.9369	8.0953	0.2536	-0.0219	-0.3521	-0.7124	-0.1982	0.2315	0.136	-0.1305	-0.0768	0.701	-0.1229	-0.1988	0.4814	-0.0798	0.9415	26.4117	-67.885	-6.5984
34	9.2676	3.7679	-0.872	7.3058	-1.9641	6.0059	0.616	0.3303	-2.384	-0.7533	-0.1842	1.0792	1.6712	-0.8382	-0.3974	1.3216	-0.3384	-0.3028	0.9452	-0.0806	1.7084	14.5494	-84.8783	-9.5077

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 1 through 70 )	A	1 - 70
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 117 )	A	71 - 117
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 169 )	A	118 - 169
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 170 through 231 )	A	170 - 231
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 232 through 279 )	A	232 - 279
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 280 through 319 )	A	280 - 319
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 320 through 388 )	A	320 - 388
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 389 through 519 )	A	389 - 519
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 520 through 564 )	A	520 - 564
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 35 )	B	1 - 35
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 36 through 68 )	B	36 - 68
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 69 through 151 )	B	69 - 151
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 152 through 232 )	B	152 - 232
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 233 through 277 )	B	233 - 277
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 278 through 319 )	B	278 - 319
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 320 through 423 )	B	320 - 423
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 424 through 522 )	B	424 - 522
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 523 through 564 )	B	523 - 564
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 1 through 34 )	C	1 - 34
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 35 through 70 )	C	35 - 70
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 71 through 117 )	C	71 - 117
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 118 through 169 )	C	118 - 169
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 170 through 231 )	C	170 - 231
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 232 through 279 )	C	232 - 279
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 280 through 319 )	C	280 - 319
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 320 through 388 )	C	320 - 388
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 389 through 519 )	C	389 - 519
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 520 through 564 )	C	520 - 564
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 1 through 113 )	D	1 - 113
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 114 through 232 )	D	114 - 232
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 233 through 319 )	D	233 - 319
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 320 through 423 )	D	320 - 423
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 424 through 522 )	D	424 - 522
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 523 through 564 )	D	523 - 564

-
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