PDB-4zqr: Crystal Structure of the Catalytic Domain of the Inosine Monophos...

ID or keywords:

Entry

Database: PDB / ID: 4zqr

Title

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis

Components

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

Keywords

OXIDOREDUCTASE / IMPDH / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

XMP biosynthetic process / IMP catabolic process / IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / peptidoglycan-based cell wall / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.692 Å

Authors

Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Kavitha, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: Plos One / Year: 2015
Title: Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds.
Authors: Makowska-Grzyska, M. / Kim, Y. / Gorla, S.K. / Wei, Y. / Mandapati, K. / Zhang, M. / Maltseva, N. / Modi, G. / Boshoff, H.I. / Gu, M. / Aldrich, C. / Cuny, G.D. / Hedstrom, L. / Joachimiak, A.

History

Deposition	May 11, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 16, 2015	Group: Database references
Revision 1.2	Feb 8, 2017	Group: Structure summary
Revision 1.3	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.4	Mar 30, 2022	Group: Author supporting evidence / Database references / Derived calculations Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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
Revision 1.5	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4zqr.cif.gz	560.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4zqr.ent.gz	463.5 KB	Display	PDB format
PDBx/mmJSON format	4zqr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4zqr_validation.pdf.gz	508.4 KB	Display	wwPDB validaton report
Full document	4zqr_full_validation.pdf.gz	527.7 KB	Display
Data in XML	4zqr_validation.xml.gz	60.8 KB	Display
Data in CIF	4zqr_validation.cif.gz	87.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zq/4zqr ftp://data.pdbj.org/pub/pdb/validation_reports/zq/4zqr	HTTPS FTP

-
Related structure data

Related structure data	4zqmC 4zqnC 4zqoC 4zqpC C: citing same article (ref.)
Similar structure data	4zqn-1 4myx-1 5urs-2 3beq-1 4wa3-1 6d96-2 3ti3-1 4mya-2 5nzf-d 5nzn-d 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: CSGID-idp91646

-
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-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

C: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

D: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	75.217, 75.233, 75.291
Angle α, β, γ (deg.)	108.30, 108.25, 111.88
Int Tables number	1
Space group name H-M	P1

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH Mass: 41642.621 Da / Num. of mol.: 4 Fragment: UNP residues 1-125 and 253-529 linked by linker (GLY GLY) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: guaB, guaB2, Rv3411c, MTCY78.17 / Plasmid: pMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: P9WKI7, IMP dehydrogenase

#1: Protein

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH

Mass: 41642.621 Da / Num. of mol.: 4
Fragment: UNP residues 1-125 and 253-529 linked by linker (GLY GLY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: guaB, guaB2, Rv3411c, MTCY78.17 / Plasmid: pMCSG7 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: P9WKI7, IMP dehydrogenase

-
Non-polymers , 5 types, 827 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-PGO / S-1,2-PROPANEDIOL Mass: 76.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 793 / 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: 1.97 Å³/Da / Density % sol: 37.46 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.1 M Na/K phosphate pH 6.2, 25 %(v/v) 1,2 propandiol, 10 %(v/v) glycerol

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2012
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.692→35.726 Å / Num. obs: 129346 / % possible obs: 91.4 % / Redundancy: 2.2 % / B_iso Wilson estimate: 21.38 Å² / R_sym value: 0.056 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 2.6 / % possible all: 51.5

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1839	refinement
SBC-Collect	dev_1839	data collection
HKL-3000		data reduction
HKL-3000		phasing
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.692→35.726 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1828	6432	4.97 %	random
R_work	0.1512	-	-	-
obs	0.1528	129299	91.21 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.692→35.726 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10171	0	165	793	11129

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11187
X-RAY DIFFRACTION	f_angle_d	1.282	15253
X-RAY DIFFRACTION	f_dihedral_angle_d	13.477	4103
X-RAY DIFFRACTION	f_chiral_restr	0.084	1812
X-RAY DIFFRACTION	f_plane_restr	0.006	2008

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 (%)
1.6916-1.7108	0.2664	107	0.2381	2097	X-RAY DIFFRACTION	46
1.7108-1.731	0.2485	135	0.2148	2559	X-RAY DIFFRACTION	57
1.731-1.7521	0.2678	161	0.2091	2811	X-RAY DIFFRACTION	63
1.7521-1.7742	0.2327	167	0.1861	3198	X-RAY DIFFRACTION	72
1.7742-1.7976	0.2151	206	0.1895	3755	X-RAY DIFFRACTION	84
1.7976-1.8222	0.2098	208	0.1812	4115	X-RAY DIFFRACTION	92
1.8222-1.8482	0.2461	211	0.1881	4264	X-RAY DIFFRACTION	94
1.8482-1.8758	0.2241	234	0.1759	4270	X-RAY DIFFRACTION	95
1.8758-1.9051	0.2199	191	0.1749	4229	X-RAY DIFFRACTION	95
1.9051-1.9364	0.1926	217	0.1676	4375	X-RAY DIFFRACTION	96
1.9364-1.9698	0.2188	248	0.1632	4290	X-RAY DIFFRACTION	96
1.9698-2.0056	0.2026	235	0.167	4259	X-RAY DIFFRACTION	96
2.0056-2.0441	0.2085	254	0.1471	4397	X-RAY DIFFRACTION	97
2.0441-2.0859	0.1972	245	0.145	4278	X-RAY DIFFRACTION	97
2.0859-2.1312	0.1757	206	0.1458	4309	X-RAY DIFFRACTION	97
2.1312-2.1808	0.1853	238	0.1468	4450	X-RAY DIFFRACTION	97
2.1808-2.2353	0.1907	238	0.1441	4382	X-RAY DIFFRACTION	97
2.2353-2.2957	0.1692	204	0.1407	4356	X-RAY DIFFRACTION	97
2.2957-2.3633	0.2006	218	0.1404	4399	X-RAY DIFFRACTION	98
2.3633-2.4395	0.1748	224	0.1464	4418	X-RAY DIFFRACTION	97
2.4395-2.5267	0.2155	233	0.1475	4377	X-RAY DIFFRACTION	98
2.5267-2.6278	0.1787	231	0.1407	4392	X-RAY DIFFRACTION	98
2.6278-2.7474	0.1745	254	0.1467	4406	X-RAY DIFFRACTION	98
2.7474-2.8922	0.1903	227	0.1515	4444	X-RAY DIFFRACTION	98
2.8922-3.0733	0.1914	211	0.1524	4345	X-RAY DIFFRACTION	98
3.0733-3.3104	0.165	233	0.1414	4453	X-RAY DIFFRACTION	98
3.3104-3.6433	0.1685	223	0.1457	4344	X-RAY DIFFRACTION	97
3.6433-4.1698	0.1595	221	0.1329	4387	X-RAY DIFFRACTION	96
4.1698-5.2508	0.1643	239	0.1414	4265	X-RAY DIFFRACTION	96
5.2508-35.734	0.1675	213	0.1718	4243	X-RAY DIFFRACTION	94

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	0.734	-0.3128	-0.2275	0.2527	-0.0148	0.738	-0.0549	-0.0794	0.002	0.0275	0.0309	-0.0075	0.0172	-0.0549	0.0482	0.1673	0.0072	0.0084	0.1621	0.0195	0.1759	17.2483	33.1245	56.2392
2	2.3818	0.2486	0.7191	1.8019	0.5491	1.5498	-0.0055	-0.3566	-0.1651	0.3022	0.0702	-0.1124	0.057	0.0694	-0.0781	0.2105	0.041	-0.0227	0.2443	0.0488	0.157	30.6763	27.4176	70.5825
3	1.6957	-0.4887	-0.2843	0.5083	0.3555	0.5925	0.0105	0.0279	-0.0059	0.0198	-0.0268	-0.0364	0.0032	-0.0114	0.0185	0.1799	0.021	-0.0139	0.1679	0.0124	0.1675	20.7125	30.4806	55.3315
4	3.2481	-1.4411	-1.9389	5.0289	3.2759	4.7804	0.0369	-0.0754	0.3475	-0.0721	0.1179	-0.5016	-0.1753	0.4906	-0.1126	0.2565	-0.0227	-0.0105	0.246	-0.0004	0.2616	35.4116	45.8061	56.3605
5	1.4306	-0.0923	0.4107	1.0822	0.0653	2.4666	-0.0286	-0.0572	0.0584	0.0084	0.0421	0.0414	-0.0933	-0.1247	-0.0315	0.136	0.0336	0.0014	0.1497	0.0039	0.1611	9.2258	40.402	54.5874
6	0.5278	0.2713	-0.8883	1.7428	-0.2312	3.5265	-0.1299	0.0122	0.23	0.0819	-0.0889	-0.2176	-0.5311	0.599	0.129	0.3243	-0.0347	-0.0329	0.3299	0.0337	0.3065	16.178	54.9701	46.6686
7	5.3444	-2.383	-3.253	1.2838	1.6085	2.3703	-0.2147	-0.0024	-0.2087	0.1164	0.0227	0.1359	0.3084	-0.0474	0.2894	0.2206	-0.0067	-0.0187	0.1865	0.0121	0.1845	9.6661	28.1274	24.6277
8	2.2338	-1.3618	0.34	2.629	-0.3935	1.2415	0.1218	0.3273	0.1674	-0.3272	-0.1251	-0.0342	-0.1004	0.0125	0.0074	0.2345	0.0266	0.0155	0.2549	0.0346	0.1489	14.6178	45.6068	-5.3067
9	1.026	-0.3385	-0.1659	1.4163	0.013	0.7461	0.0013	0.1435	-0.0318	-0.1161	0.0015	0.1392	-0.029	-0.0396	0.0071	0.1539	0.015	-0.0157	0.1809	0.0154	0.1613	6.8128	37.9052	6.2626
10	4.6199	-0.4349	-3.4121	3.2746	0.1793	4.7054	0.1566	-0.0369	0.5762	0.012	0.0225	-0.1774	-0.5737	0.0386	-0.1313	0.2883	-0.0289	-0.0024	0.2418	0.0076	0.2539	20.0649	55.9236	10.2582
11	1.3077	-0.2161	0.0496	3.5772	-1.2606	2.8266	0.0674	0.1914	0.142	-0.406	-0.1085	-0.2775	0.0339	0.2313	0.0439	0.1636	0.0331	0.0298	0.2518	0.0173	0.1955	29.9311	33.7506	5.4472
12	1.721	0.1751	0.7019	1.0341	0.1443	3.3475	-0.0193	-0.0121	0.1362	0.0476	-0.0132	-0.1047	-0.2396	0.1566	0.0029	0.1715	0.0493	-0.0079	0.1477	0.0151	0.1841	27.8721	32.4508	17.9689
13	6.8893	2.2474	5.1314	1.2018	1.927	3.925	0.3188	-0.5249	-0.6475	0.1655	-0.0925	0.0004	0.3359	-0.3485	-0.3133	0.2156	-0.023	-0.0085	0.2108	0.0375	0.227	12.5451	22	22.8952
14	1.0296	-0.0462	-0.6243	0.4906	-0.0943	1.8269	-0.0471	0.0482	-0.0493	-0.0712	-0.0247	-0.1499	0.1892	0.2992	0.0758	0.2017	0.045	0.0144	0.2291	0.0028	0.2225	48.7131	17.9375	24.9271
15	0.6241	0.1677	0.1244	0.807	-0.3304	1.9758	-0.0101	0.0076	-0.036	-0.0469	0.0251	-0.0956	0.0751	0.0427	-0.0234	0.1441	0.0174	0.0085	0.1666	-0.0061	0.1545	35.8263	18.2003	26.0477
16	5.107	-0.7267	3.2992	1.8399	-1.0395	4.5669	-0.0383	0.3125	0.3997	-0.1425	-0.0723	-0.1891	-0.3385	0.3278	0.0236	0.2292	-0.0192	0.0117	0.2451	0.0317	0.2825	46.9809	37.7018	24.2138
17	3.5095	0.5234	-1.4364	2.007	-0.5473	2.2341	-0.1088	-0.3046	-0.14	0.0734	-0.0581	-0.2901	0.0334	0.3937	-0.0037	0.1711	0.0263	-0.0387	0.2474	0.0059	0.1715	43.6858	24.4331	44.4744
18	2.1681	-0.944	-0.1388	2.5344	0.8007	1.6485	0.0557	0.0137	0.2397	-0.0639	-0.0563	-0.0764	-0.2103	0.0476	-0.0178	0.1843	0.0066	0.0258	0.2052	0.0311	0.1381	31.9638	29.7985	43.3129
19	0.6566	-0.4015	0.3785	0.1769	-0.2809	1.1618	0.0525	0.0229	-0.0947	-0.0406	-0.0166	0.0802	0.0549	-0.0847	-0.0689	0.1373	-0.0139	-0.0085	0.1388	-0.0023	0.1533	-2.1437	40.3842	33.0228
20	2.3766	-0.2967	0.3526	2.0439	0.0954	5.266	-0.0134	0.0105	0.3752	-0.0141	-0.0469	0.0877	-0.6758	-0.2259	0.0663	0.2598	0.0587	-0.0044	0.1509	0.0007	0.2498	-7.5559	66.7626	42.1807
21	2.5883	-0.937	-0.0841	4.5706	0.535	1.5127	0.0041	-0.1148	0.1913	0.3787	-0.0815	0.2755	-0.0412	-0.3746	0.0361	0.196	0.0373	0.0448	0.2595	-0.0345	0.1675	-13.9662	56.0081	51.4978
22	1.0753	-0.3695	0.2423	1.03	-0.2174	1.7613	0.0109	-0.0003	0.1938	0.0243	-0.0432	-0.0288	-0.1671	0.0252	0.0067	0.1411	0.0208	0.0101	0.1347	0.0038	0.1321	-1.493	51.1481	39.8278
23	1.5334	0.1912	1.638	2.1535	-0.0165	2.5059	-0.1712	-0.2054	0.1828	0.1464	-0.0001	-0.091	-0.5035	-0.1952	0.1302	0.1422	0.0646	0.0397	0.227	0.0117	0.2023	3.704	57.992	37.0852
24	2.8474	-0.5492	-0.6522	1.0636	-0.0101	1.2436	0.0051	-0.0657	0.2361	-0.0475	0.0217	-0.1265	-0.0684	0.1328	-0.0364	0.2023	0.012	-0.0096	0.1856	-0.0148	0.1611	6.7951	46.2607	23.2744

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 27 through 99 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 100 through 326 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 327 through 396 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 397 through 469 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 470 through 512 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 513 through 528 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 27 through 60 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 61 through 275 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 276 through 396 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 397 through 469 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 470 through 488 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 489 through 528 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 26 through 46 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 47 through 303 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 304 through 396 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 397 through 469 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 470 through 488 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 489 through 528 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 27 through 82 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 83 through 125 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 126 through 303 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 304 through 422 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 423 through 488 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 489 through 528 )

-
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 , 5 types, 827 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 , 5 types, 827 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 , 5 types, 827 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