PDB-6mgr: Crystal Structure of the Catalytic Domain of the Inosine Monophos...

ID or keywords:

Entry

Database: PDB / ID: 6mgr

Title

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine monophosphate

Components

Inosine monophosphate dehydrogenase

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / TIM barrel / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Kim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine Monophosphate
Authors: Kim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Sep 14, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6mgr.cif.gz	571.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6mgr.ent.gz	471.3 KB	Display	PDB format
PDBx/mmJSON format	6mgr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgr ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgr	HTTPS FTP

-
Related structure data

Related structure data	5urqS S: Starting model for refinement
Similar structure data	6a08-1 5uqh-2 5uqg-2 5uqg-1 5uqh-1 4gdi-3 4mz1-3 5uqf-2 4mz1-1 4mz8-2 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	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4)

Deposited unit

A: Inosine monophosphate dehydrogenase

B: Inosine monophosphate dehydrogenase

C: Inosine monophosphate dehydrogenase

D: Inosine monophosphate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	69.343, 119.592, 119.307
Angle α, β, γ (deg.)	90.00, 89.99, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Inosine monophosphate dehydrogenase / IMP dehydrogenase Mass: 41053.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: C9J79_08320 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2R4D3F6, IMP dehydrogenase

#1: Protein

Inosine monophosphate dehydrogenase / IMP dehydrogenase

Mass: 41053.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni (Campylobacter) / Gene: C9J79_08320 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2R4D3F6, IMP dehydrogenase

-
Non-polymers , 6 types, 467 molecules

#2: Chemical	ChemComp-JQS / 5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid Mass: 366.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₄O₉P
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.01 Å³/Da / Density % sol: 59.17 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M Lithium Sulfate, 0.1 M MES:NaOH pH 6, 35% (v/v) MPD

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 1.97→50 Å / Num. obs: 135052 / % possible obs: 98.2 % / Redundancy: 5.7 % / R_merge(I) obs: 0.131 / Net I/σ(I): 17
Reflection shell	Resolution: 1.97→2 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.876 / Mean I/σ(I) obs: 1 / Num. unique obs: 5909 / CC_1/2: 0.591 / % possible all: 86.7

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBID 5URQ

5urq

Resolution: 1.97→45.284 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 23.88

	R_factor	Num. reflection	% reflection
R_free	0.2018	6506	4.84 %
R_work	0.1734	-	-
obs	0.1749	134425	97.44 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→45.284 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10843	0	220	428	11491

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11300
X-RAY DIFFRACTION	f_angle_d	0.96	15256
X-RAY DIFFRACTION	f_dihedral_angle_d	16.308	6828
X-RAY DIFFRACTION	f_chiral_restr	0.053	1753
X-RAY DIFFRACTION	f_plane_restr	0.004	1942

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 (%)
1.9662-1.9886	0.4166	164	0.3597	3202	X-RAY DIFFRACTION	74
1.9886-2.012	0.3594	190	0.3211	3684	X-RAY DIFFRACTION	86
2.012-2.0365	0.3514	178	0.305	3969	X-RAY DIFFRACTION	90
2.0365-2.0623	0.295	191	0.2833	4129	X-RAY DIFFRACTION	94
2.0623-2.0894	0.2796	222	0.2567	4197	X-RAY DIFFRACTION	96
2.0894-2.118	0.2986	198	0.2442	4230	X-RAY DIFFRACTION	98
2.118-2.1483	0.2465	224	0.2404	4314	X-RAY DIFFRACTION	98
2.1483-2.1804	0.2637	278	0.2298	4297	X-RAY DIFFRACTION	99
2.1804-2.2144	0.2826	219	0.2211	4266	X-RAY DIFFRACTION	99
2.2144-2.2507	0.2352	219	0.1921	4355	X-RAY DIFFRACTION	100
2.2507-2.2896	0.2023	177	0.1873	4390	X-RAY DIFFRACTION	99
2.2896-2.3312	0.2201	221	0.198	4350	X-RAY DIFFRACTION	100
2.3312-2.376	0.2544	190	0.1828	4415	X-RAY DIFFRACTION	100
2.376-2.4245	0.2095	198	0.1885	4359	X-RAY DIFFRACTION	100
2.4245-2.4772	0.2177	185	0.188	4413	X-RAY DIFFRACTION	100
2.4772-2.5349	0.2423	207	0.1885	4352	X-RAY DIFFRACTION	100
2.5349-2.5982	0.238	215	0.1954	4365	X-RAY DIFFRACTION	100
2.5982-2.6685	0.2541	260	0.1832	4289	X-RAY DIFFRACTION	99
2.6685-2.747	0.2488	208	0.1925	4290	X-RAY DIFFRACTION	99
2.747-2.8356	0.2559	212	0.2034	4376	X-RAY DIFFRACTION	100
2.8356-2.937	0.213	179	0.2027	4465	X-RAY DIFFRACTION	100
2.937-3.0545	0.212	219	0.2021	4363	X-RAY DIFFRACTION	100
3.0545-3.1935	0.2336	263	0.1961	4320	X-RAY DIFFRACTION	100
3.1935-3.3618	0.2166	264	0.1856	4314	X-RAY DIFFRACTION	99
3.3618-3.5724	0.2137	230	0.1653	4348	X-RAY DIFFRACTION	99
3.5724-3.8481	0.1676	205	0.1548	4431	X-RAY DIFFRACTION	100
3.8481-4.2351	0.1574	217	0.14	4380	X-RAY DIFFRACTION	100
4.2351-4.8473	0.1661	217	0.1334	4373	X-RAY DIFFRACTION	100
4.8473-6.1047	0.1807	321	0.1571	4300	X-RAY DIFFRACTION	99
6.1047-45.2964	0.1837	235	0.1634	4383	X-RAY DIFFRACTION	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	1.5642	-0.5684	-0.7868	0.8524	0.3358	3.4969	-0.0645	-0.0634	-0.1449	0.091	-0.0052	0.2313	0.1641	-0.165	0.1339	0.4275	-0.047	0.0388	0.4195	0.0174	0.4476	20.4435	9.3209	50.2442
2	6.2577	0.9223	0.5518	2.1423	3.8002	8.2153	-0.0704	-0.2541	-1.1794	0.4477	-0.146	1.177	1.0301	-0.8352	0.1194	0.6703	-0.1512	0.1283	0.8453	0.1498	0.7875	8.9296	0.8094	66.1291
3	2.0687	0.7038	0.4847	9.127	3.1106	4.6446	-0.0768	-0.3767	-0.2846	0.6093	0.0866	0.2635	0.6392	-0.4064	0.0246	0.5549	-0.0712	0.1694	0.5394	0.0774	0.5008	17.5814	6.3845	67.8592
4	0.6274	0.6648	0.3098	1.2917	-0.1923	1.4733	-0.0482	-0.0563	0.003	0.0877	0.0307	0.0921	-0.1491	-0.1022	0.0014	0.4653	0.0232	0.0802	0.4027	0.0174	0.383	25.6472	17.7754	56.3231
5	5.3585	1.2872	0.1952	3.2269	1.889	3.2354	-0.1085	-0.3184	0.4716	-0.4108	-0.0226	0.4641	-0.3894	-0.9096	0.0822	0.51	-0.0259	0.0056	0.8905	0.0168	0.8206	-1.6216	15.6401	49.9913
6	1.7711	1.3179	0.1536	4.1745	1.3113	3.6575	0.8735	-0.2461	-0.2249	0.9133	-0.6745	0.1001	-0.2991	-0.6469	0.045	0.977	0.0506	0.1738	0.8934	0.0606	0.7671	11.1732	30.5203	60.0452
7	4.4962	-1.6835	-1.9937	3.1676	1.6582	2.5049	-0.0507	0.2101	-0.3279	-0.3757	-0.0337	0.3178	0.3578	-0.4122	0.1377	0.5522	-0.1349	-0.0265	0.4904	0.0335	0.4704	11.9276	6.5255	43.9235
8	3.3633	-0.4066	0.3217	3.8237	-1.03	4.3119	0.0401	0.2846	-0.0213	0.0357	-0.0241	0.491	-0.1054	-0.4592	0.004	0.5208	0.0027	0.1131	0.4468	-0.069	0.428	19.6832	10.9117	33.7994
9	1.4632	-0.2109	0.7495	2.6575	-0.1581	1.4775	-0.0739	-0.1562	0.1277	0.1954	0.0454	0.2764	-0.1961	-0.245	0.0148	0.3912	0.0405	0.0754	0.4237	-0.0123	0.3795	18.9513	52.6817	49.8498
10	2.3544	-0.8975	2.1729	8.2672	-2.1444	3.222	0.088	-0.7186	0.3857	0.8357	0.2979	0.6678	-0.5834	-0.8046	-0.3259	0.8199	0.1356	0.2058	0.7789	-0.0707	0.5118	14.3354	61.6332	64.2722
11	0.8277	0.2415	-0.407	1.5655	0.1062	1.5833	-0.0655	-0.0126	0.0956	-0.0363	0.0412	0.1331	-0.1539	-0.1021	0.028	0.4552	0.0535	0.0119	0.3955	-0.0206	0.4157	24.7447	58.1658	41.8335
12	5.2357	0.913	-3.1298	2.6716	-2.6585	5.842	-0.1163	0.6049	0.3301	-0.2199	0.2606	0.7929	0.2363	-0.8812	-0.3234	0.4758	-0.002	0.0387	0.8997	0.0092	0.8235	-1.779	50.0354	43.78
13	1.7811	-0.4086	0.8796	2.2507	-0.0938	2.6525	0.1053	0.1208	0.1328	-0.2105	-0.1434	0.3938	-0.1727	-0.2975	0.0187	0.6001	0.034	0.1149	0.5457	-0.0185	0.5743	11.6223	50.0293	43.1825
14	3.5669	1.3805	1.3009	5.0242	1.7648	4.9681	0.0038	-0.2188	-0.1699	-0.2312	-0.0604	0.5095	-0.1332	-0.6171	0.0465	0.4473	0.1099	0.0448	0.4182	0.0853	0.4295	19.8576	33.4052	48.5284
15	1.6584	0.69	0.1577	1.0049	0.2048	3.3806	-0.0782	0.2045	0.2179	-0.1951	0.0441	0.3101	-0.285	-0.286	0.0314	0.397	0.0609	-0.032	0.3685	0.0376	0.4395	17.9029	51.4288	2.6257
16	0.9821	-0.4014	0.0255	1.7996	-0.0384	2.0855	-0.0521	0.0059	-0.0559	-0.075	0.0325	0.2524	0.0728	-0.2686	0.0311	0.3981	-0.0093	-0.0273	0.4077	0.0129	0.4101	21.0466	41.5212	4.3335
17	0.5164	0.3773	0.9804	1.3134	0.0409	1.5783	0.2321	0.4763	-0.1522	-0.5491	-0.1924	0.0335	0.327	-0.5936	-0.0786	0.8542	0.0179	-0.0656	0.9838	0.0057	0.7824	8.6326	31.8431	0.6083
18	1.0242	-0.8504	0.5152	3.2652	-1.5919	4.8489	0.1419	-0.3018	-0.0007	0.0938	0.0264	0.4095	-0.0427	-0.4406	-0.2135	0.4246	0.0279	0.0191	0.4151	-0.0605	0.413	18.8689	50.7929	23.3185
19	1.2838	0.3099	-0.5082	2.7638	0.0257	1.0691	-0.0514	0.1812	-0.0536	-0.1874	0.0694	0.1384	0.1093	-0.1672	-0.0098	0.4173	-0.0126	-0.0273	0.4365	-0.0129	0.3931	20.5843	9.075	9.9684
20	2.4847	-0.1376	0.926	4.2781	-1.2299	5.2216	-0.1476	0.9176	-0.3284	-0.9809	0.0667	0.8361	0.4987	-1.161	0.075	0.6635	-0.1383	-0.1059	0.8003	-0.12	0.7534	8.9397	-7.1677	1.8986
21	2.0792	0.1942	0.512	3.498	-0.9569	5.8443	-0.1056	0.3211	-0.2508	-0.4748	0.0085	0.3426	0.3952	-0.2553	0.0726	0.5261	-0.1079	-0.021	0.5344	-0.0896	0.5699	17.5656	-8.6269	6.7714
22	0.5745	-0.4797	0.0981	1.7126	-0.0878	1.6772	-0.0444	0.0038	-0.0549	0.079	-0.0265	0.1379	0.1297	-0.0548	0.0608	0.4538	-0.0453	0.0349	0.4117	-0.0206	0.4434	25.6458	2.948	18.1373
23	9.8467	-3.2443	1.9969	4.4603	-3.6865	5.7786	-0.4749	-0.7606	0.0069	0.5933	0.5696	0.9918	-0.3138	-1.0538	-0.0721	0.5019	-0.0155	0.0203	0.9202	0.0179	0.9209	-1.6006	9.2587	15.9071
24	3.1081	-1.2114	3.9705	6.2891	-0.1275	5.4836	1.048	0.2249	-0.5849	0.3599	-0.1829	0.8125	1.0056	0.1772	-0.4907	0.9569	-0.1621	0.0594	0.9103	-0.0413	0.8689	11.1837	-0.7972	30.827
25	5.3243	1.4843	-2.1431	2.2502	-1.0906	3.2455	0.1127	0.3425	0.1567	-0.2922	-0.0268	0.3569	-0.3653	-0.4213	-0.0303	0.5389	0.0587	-0.1117	0.4726	-0.0267	0.5091	11.9355	15.3749	6.8941
26	3.8256	-1.2331	-0.4096	4.7163	2.0811	4.8871	-0.0507	0.1397	0.1317	0.2198	-0.0423	0.5806	0.0525	-0.5518	0.0674	0.4613	-0.092	0.0344	0.3627	0.0992	0.446	20.2542	25.078	10.8899

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 74 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 75 through 204 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 205 through 235 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 236 through 361 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 362 through 382 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 383 through 413 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 414 through 441 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 442 through 482 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 0 through 86 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 87 through 217 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 218 through 361 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 362 through 382 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 383 through 441 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 442 through 481 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 0 through 235 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 236 through 382 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 383 through 422 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 423 through 481 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 0 through 74 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 75 through 204 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 205 through 235 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 236 through 361 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 362 through 382 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 383 through 413 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 414 through 441 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 442 through 481 )

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 467 molecules

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 6 types, 467 molecules

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 467 molecules

-
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