PDB-4z87: Structure of the IMP dehydrogenase from Ashbya gossypii bound to GDP

ID or keywords:

Entry

Database: PDB / ID: 4z87

Title

Structure of the IMP dehydrogenase from Ashbya gossypii bound to GDP

Components

Inosine-5'-monophosphate dehydrogenase

Keywords

OXIDOREDUCTASE / IMP dehydrgoenase / Bateman domain

Function / homology

Function and homology information

IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Ashbya gossypii (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Buey, R.M. / de Pereda, J.M. / Revuelta, J.L.

Citation

Journal: Nat Commun / Year: 2015
Title: Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases.
Authors: Buey, R.M. / Ledesma-Amaro, R. / Velazquez-Campoy, A. / Balsera, M. / Chagoyen, M. / de Pereda, J.M. / Revuelta, J.L.

History

Deposition	Apr 8, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4z87.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb4z87.ent.gz	912.9 KB	Display	PDB format
PDBx/mmJSON format	4z87.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4z87_validation.pdf.gz	6.4 MB	Display	wwPDB validaton report
Full document	4z87_full_validation.pdf.gz	6.3 MB	Display
Data in XML	4z87_validation.xml.gz	74.7 KB	Display
Data in CIF	4z87_validation.cif.gz	100.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/4z87 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/4z87	HTTPS FTP

-
Related structure data

Related structure data	4z0gSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5tc3-1 6jig-1 6ua4-d 6udo-d 20743 1zfj-2 6u9o-d 6udq-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4z0gSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1)

Deposited unit

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

C: Inosine-5'-monophosphate dehydrogenase

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

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

1

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by software
OCTAMERIC
469 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by software
OCTAMERIC
469 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_645	-x+1,-y-1,z	1
crystal symmetry operation	3_545	-y,x-1,z	1
crystal symmetry operation	4_655	y+1,-x,z	1
crystal symmetry operation	1_554	x,y,z-1	1
crystal symmetry operation	2_644	-x+1,-y-1,z-1	1
crystal symmetry operation	3_544	-y,x-1,z-1	1
crystal symmetry operation	4_654	y+1,-x,z-1	1

3

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

C: Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by software
OCTAMERIC
469 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_655	y+1,-x,z	1
crystal symmetry operation	2_645	-x+1,-y-1,z	1
crystal symmetry operation	3_545	-y,x-1,z	1
crystal symmetry operation	3_546	-y,x-1,z+1	1
crystal symmetry operation	1_556	x,y,z+1	1
crystal symmetry operation	2_646	-x+1,-y-1,z+1	1
crystal symmetry operation	4_656	y+1,-x,z+1	1

Unit cell

Length a, b, c (Å)	122.042, 122.042, 147.613
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	75
Space group name H-M	P4

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Inosine-5'-monophosphate dehydrogenase / IMPDH Mass: 56808.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895) (fungus) Gene: AGOS_AER117W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q756Z6, IMP dehydrogenase

-
Non-polymers , 5 types, 471 molecules

#2: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P
#3: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.15 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 40% (v/v) 1,2-propanediol, 0.1 M sodium acetate, pH 4.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 22, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00004 Å / Relative weight: 1
Reflection	Resolution: 2.25→47.05 Å / Num. obs: 102432 / % possible obs: 100 % / Redundancy: 13.84 % / R_merge(I) obs: 0.11 / Net I/σ(I): 26.04
Reflection shell	Resolution: 2.25→2.31 Å / Redundancy: 14.15 % / R_merge(I) obs: 1.65 / Mean I/σ(I) obs: 1.98 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1839	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z0G

4z0g

Resolution: 2.25→47.029 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2254	5017	4.91 %
R_work	0.1949	-	-
obs	0.1964	102236	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.25→47.029 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14567	0	452	447	15466

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15389
X-RAY DIFFRACTION	f_angle_d	0.737	20857
X-RAY DIFFRACTION	f_dihedral_angle_d	11.497	5502
X-RAY DIFFRACTION	f_chiral_restr	0.028	2420
X-RAY DIFFRACTION	f_plane_restr	0.003	2632

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 (%)
2.25-2.2756	0.3349	170	0.2805	3202	X-RAY DIFFRACTION	100
2.2756-2.3024	0.262	155	0.2627	3280	X-RAY DIFFRACTION	100
2.3024-2.3304	0.3074	179	0.2602	3201	X-RAY DIFFRACTION	100
2.3304-2.3599	0.2951	198	0.2554	3185	X-RAY DIFFRACTION	100
2.3599-2.391	0.2886	154	0.2493	3269	X-RAY DIFFRACTION	100
2.391-2.4237	0.2745	176	0.2476	3201	X-RAY DIFFRACTION	100
2.4237-2.4584	0.2682	139	0.2396	3280	X-RAY DIFFRACTION	100
2.4584-2.4951	0.289	171	0.2372	3215	X-RAY DIFFRACTION	100
2.4951-2.534	0.2789	150	0.2345	3220	X-RAY DIFFRACTION	100
2.534-2.5756	0.2814	161	0.2345	3243	X-RAY DIFFRACTION	100
2.5756-2.62	0.2309	200	0.2264	3199	X-RAY DIFFRACTION	100
2.62-2.6676	0.2705	203	0.2249	3207	X-RAY DIFFRACTION	100
2.6676-2.7189	0.2767	130	0.2287	3287	X-RAY DIFFRACTION	100
2.7189-2.7744	0.2663	135	0.2185	3262	X-RAY DIFFRACTION	100
2.7744-2.8348	0.2766	148	0.2227	3236	X-RAY DIFFRACTION	100
2.8348-2.9007	0.2724	185	0.2225	3231	X-RAY DIFFRACTION	100
2.9007-2.9732	0.2637	135	0.2177	3266	X-RAY DIFFRACTION	100
2.9732-3.0536	0.2395	172	0.2183	3217	X-RAY DIFFRACTION	100
3.0536-3.1434	0.2456	189	0.2086	3227	X-RAY DIFFRACTION	100
3.1434-3.2449	0.2224	168	0.2081	3234	X-RAY DIFFRACTION	100
3.2449-3.3608	0.2366	161	0.1973	3241	X-RAY DIFFRACTION	100
3.3608-3.4953	0.2091	182	0.184	3246	X-RAY DIFFRACTION	100
3.4953-3.6543	0.1981	191	0.1759	3196	X-RAY DIFFRACTION	100
3.6543-3.8469	0.185	149	0.1703	3267	X-RAY DIFFRACTION	100
3.8469-4.0878	0.1899	181	0.1656	3232	X-RAY DIFFRACTION	100
4.0878-4.4032	0.1919	179	0.1581	3213	X-RAY DIFFRACTION	100
4.4032-4.8459	0.1795	169	0.1511	3287	X-RAY DIFFRACTION	100
4.8459-5.5462	0.1973	162	0.1741	3266	X-RAY DIFFRACTION	100
5.5462-6.984	0.2322	167	0.2007	3268	X-RAY DIFFRACTION	100
6.984-47.0393	0.2331	158	0.1949	3341	X-RAY DIFFRACTION	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	2.4268	1.7908	0.0161	2.8832	0.8486	0.6061	0.0025	-0.3229	-0.0452	0.1771	-0.0583	-0.1025	0.0786	0.0914	0.0743	0.3131	-0.0101	-0.0087	0.2838	0.009	0.2805	21.3715	-4.8048	-17.2592
2	0.8538	-1.0309	-0.9026	1.5043	1.463	1.5646	-0.0028	0.139	-0.2097	-0.1022	-0.0943	0.1688	0.0204	-0.1395	0.1148	0.3566	-0.0012	-0.0213	0.2399	-0.0096	0.4185	16.8422	-47.3076	-44.0476
3	1.9396	0.2427	-0.6121	1.3943	0.5192	2.0651	0.0012	0.2832	-0.0865	-0.3548	0.0227	0.0837	-0.1209	-0.3581	-0.0231	0.3067	0.0234	-0.0159	0.2094	0.0034	0.2851	7.6598	-24.513	-33.6729
4	2.4525	0.1017	-0.12	1.5283	0.0951	1.3963	-0.2095	0.7324	0.5128	-0.7961	-0.2803	-0.3218	-0.0581	-0.2979	0.3776	0.7083	0.0232	0.0602	0.4965	0.0135	0.5474	14.8666	-5.2945	-34.503
5	4.2811	1.8946	0.6308	2.3006	0.1839	2.1809	-0.6555	1.0986	0.0367	-0.7198	0.6499	-0.107	-0.0297	0.1185	0.1008	0.4458	-0.0092	-0.0375	0.5138	0.0306	0.2962	-2.6656	-19.3187	-99.6201
6	2.5457	-1.2183	1.2054	0.6704	-0.8201	0.9653	-0.0729	-0.187	-0.0917	0.15	0.0831	-0.1067	0.0433	-0.0752	-0.0068	0.3072	0.0536	-0.026	0.3283	-0.0389	0.3349	27.1873	-23.9121	-76.7287
7	2.231	0.4856	0.2758	1.9021	-0.4374	2.9097	0.2042	-0.2689	-0.1162	0.0648	-0.1946	-0.1772	0.0102	0.5395	-0.0071	0.2911	0.0348	-0.0358	0.4513	-0.0229	0.3548	48.8013	-40.762	-56.0703
8	0.6212	-1.5032	1.0884	3.3476	-2.3791	2.0426	0.0375	0.1601	0.0994	-0.1432	-0.1223	-0.3083	0.0621	0.2728	0.1099	0.3061	0.0221	0.0123	0.4117	-0.0547	0.3785	36.9671	-23.134	-79.7354
9	1.6496	-0.5028	0.089	1.3064	-0.3995	1.9414	-0.0419	-0.2563	0.1432	0.1442	0.0492	-0.0407	-0.2065	0.0619	-0.0402	0.4003	0.0111	0.0165	0.4083	-0.0931	0.3786	19.5139	-12.8434	-77.9936
10	1.527	0.2175	-0.3744	0.5636	0.6788	1.6579	-0.0533	-0.3695	0.453	-0.1432	-0.1556	-0.0493	-0.5979	0.0241	0.1732	0.6018	-0.0465	-0.0718	0.6512	0.0776	0.5709	18.3739	-17.4066	-72.325
11	2.6987	-0.1763	-0.0398	1.5096	-0.3765	1.5032	-0.0626	-0.0183	0.3699	0.2146	-0.0974	0.265	-0.2756	-0.5868	0.225	0.5114	0.0266	0.0198	0.5384	-0.055	0.4749	4.5447	-19.2797	-84.0721
12	0.9988	0.7378	0.0158	2.7038	-1.0133	0.872	-0.0757	0.0769	0.2223	-0.1495	-0.0911	-0.065	-0.0849	-0.0481	0.1674	0.4414	0.0518	-0.0776	0.3273	-0.0135	0.3309	48.0877	-34.177	-102.5352
13	1.9935	-0.2958	1.1306	1.7227	-0.4917	2.503	-0.5682	0.0475	0.6353	0.2283	0.117	-0.3572	-1.0912	0.374	0.4307	0.9874	-0.0643	-0.2317	0.5007	0.1009	0.7621	43.7525	0.2729	-127.2752
14	1.5023	-0.2823	0.8279	1.7875	-1.0157	2.0082	-0.0919	0.218	0.2957	-0.1052	-0.1344	-0.3126	-0.1773	0.25	0.2148	0.4697	-0.0052	-0.0423	0.3978	0.0233	0.4221	58.963	-27.2967	-104.7147
15	0.8883	0.1388	0.0174	0.4921	-0.0023	2.0511	-0.2462	0.4336	-0.1395	-0.4464	0.131	-0.5311	0.136	0.5092	-0.0026	0.8317	-0.0313	-0.0349	0.6883	-0.0205	0.6767	54.9625	-36.807	-114.4808
16	2.5202	0.5875	-0.4886	2.3398	-0.0327	1.4245	-0.1329	0.1845	-0.3444	-0.1935	-0.1075	-0.0877	0.3867	0.0197	0.2999	0.5549	0.024	-0.049	0.4595	-0.0156	0.5282	45.4041	-48.4061	-101.6682
17	2.1607	0.4734	0.3607	2.1456	-0.0875	1.315	-0.2481	0.7966	0.1346	-0.4916	0.347	-0.0984	-0.2893	0.1571	-0.0858	0.4757	-0.0676	0.0326	0.5582	0.0017	0.2533	67.1614	-40.6148	-23.8268
18	2.3906	-1.1538	-0.6297	2.0059	0.904	0.8697	-0.1239	-0.3303	0.2441	0.0535	0.0751	0.2232	-0.0431	0.0602	0.0857	0.3467	0.0308	-0.013	0.4536	0.0219	0.3165	37.0791	-33.4517	-0.656
19	2.0923	-0.7616	-0.3227	2.404	0.7055	2.0798	-0.2569	-0.1133	-0.0357	0.3899	0.1329	0.4347	0.1225	-0.2695	0.0754	0.5887	0.1059	0.0718	0.5481	0.0727	0.6435	18.3951	-13.5926	20.0091
20	0.9381	-0.5163	-0.679	2.4798	0.7845	1.8205	0.0655	0.2123	0.4177	-0.0389	0.0183	0.1316	-0.4434	-0.3798	-0.0629	0.6336	0.0711	-0.051	0.5979	0.0501	0.5801	27.9233	-13.5248	4.2861
21	2.7	-1.5778	-0.7828	3.1586	1.522	1.6635	-0.103	0.0686	-0.1491	0.0584	-0.0345	0.39	0.1682	-0.0924	0.1062	0.4861	-0.0243	-0.063	0.436	0.0687	0.3825	30.3638	-46.6849	-9.7256
22	1.922	0.5819	0.3274	2.0752	0.7575	1.2615	0.0393	-0.7232	-0.2997	0.3186	-0.0563	0.0378	0.3815	-0.0007	0.1236	0.4514	0.019	-0.0021	0.6542	0.0591	0.3974	45.429	-40.7894	3.1334
23	3.0507	-0.3126	0.0673	2.7307	0.6356	0.4548	-0.1311	-0.0137	-0.3206	0.4229	0.0797	-0.2659	0.4019	0.0281	-0.0588	0.6909	-0.0073	0.0411	0.5637	0.0506	0.4844	59.3482	-41.7413	-8.8915

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 51 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 296 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 297 through 491 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 492 through 522 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 37 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 38 through 124 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 125 through 195 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 196 through 335 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 336 through 415 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 416 through 478 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 479 through 522 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 124 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 125 through 219 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 220 through 410 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 411 through 478 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 479 through 522 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 37 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 38 through 124 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 125 through 195 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 196 through 249 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 250 through 360 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 361 through 478 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 479 through 517 )

-
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://pdbjlvh1.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, 471 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, 471 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, 471 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