PDB-6mfu: Crystal structure of a Guanylate kinase from Cryptococcus neoform...

ID or keywords:

Entry

Database: PDB / ID: 6mfu

Title

Crystal structure of a Guanylate kinase from Cryptococcus neoformans var. grubii serotype A in complex with GDP and ADP

Components

Guanylate kinase

Keywords

HYDROLASE / SSGCID /

Cryptococcus neoformans /

Guanylate kinase /

ADP / GDP /

structural genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

guanylate kinase /

guanylate kinase activity /

Biological species

Cryptococcus neoformans var. grubii serotype A (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of a Guanylate kinase from Cryptococcus neoformans var. grubii serotype A in complex with GDP and ADP
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Sep 12, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6mfu.cif.gz	386.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6mfu.ent.gz	317.6 KB	Display	PDB format
PDBx/mmJSON format	6mfu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	1oy0-3 1y89-d 1h31-1 6jo3-1 5jd0-d 4xpu-d 3f9o-2 5mk7-d 4ohq-d 3qh2-1 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
Other databases	TargetTrack: SSGCID-CrneC.00217.a TargetTrack: CrneC.00217.a

-
Links

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

Deposited unit

A: Guanylate kinase

B: Guanylate kinase

C: Guanylate kinase

D: Guanylate kinase

hetero molecules

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

1

A: Guanylate kinase

D: Guanylate kinase

hetero molecules

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

2

B: Guanylate kinase

C: Guanylate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.670, 99.150, 90.050
Angle α, β, γ (deg.)	90.000, 91.230, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Guanylate kinase / / CrneC.00217.a Mass: 25135.643 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_01364 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: J9VQ84
#2: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1228 / 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: 2.61 Å³/Da / Density % sol: 52.9 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Microlytic MCSG1 screen, C4: 25.5% PEG 3350, 170mM Ammonium Acetate, 15% glycerol, 100mM Ammonium acetate/HCl pH 4.6: CrneC.00217.a.B1.PW38472 at 15.5mg/ml + 4mM ADP + 4mM GDP + 4mM MgCl2: ...Details: Microlytic MCSG1 screen, C4: 25.5% PEG 3350, 170mM Ammonium Acetate, 15% glycerol, 100mM Ammonium acetate/HCl pH 4.6: CrneC.00217.a.B1.PW38472 at 15.5mg/ml + 4mM ADP + 4mM GDP + 4mM MgCl2: cryo: direct: tray 301682c4, puck xcr5-9: for phasing a crystal from the same drop was incubated for 20sec each in reservoir + compounds + 5% 5M NaI in EG and 10% 5M NaI in EG, and directly vitrified, puck: TDC2-4

Crystal

Density Matthews: 2.61 Å³/Da / Density % sol: 52.9 %

Crystal grow

Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Microlytic MCSG1 screen, C4: 25.5% PEG 3350, 170mM Ammonium Acetate, 15% glycerol, 100mM Ammonium acetate/HCl pH 4.6: CrneC.00217.a.B1.PW38472 at 15.5mg/ml + 4mM ADP + 4mM GDP + 4mM MgCl2: ...

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	ALS	5.0.1		1	0.97741
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	Sep 1, 2018
RIGAKU SATURN 944+	2	CCD	Sep 5, 2018

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Single crystal, cylindrically bent, Si(220)	SINGLE WAVELENGTH	M	x-ray	1
2	RIGAKU VARIMAX	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97741	1
2	1.5418	1

Reflection

Resolution: 1.6→49.575 Å / Num. obs: 131080 / % possible obs: 96.7 % / Redundancy: 3.253 % / B_iso Wilson estimate: 27.655 Å² / CC_1/2: 1 / R_merge(I) obs: 0.021 / R_rim(I) all: 0.025 / Χ²: 1.03 / Net I/σ(I): 30.65

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
1.6-1.64	2.597	0.201	4.4	8917	0.948	0.247	89.6
1.64-1.69	2.907	0.167	5.7	9227	0.965	0.204	94.8
1.69-1.74	3.285	0.14	7.5	9027	0.979	0.166	95.4
1.74-1.79	3.432	0.113	9.64	8885	0.986	0.133	96.4
1.79-1.85	3.347	0.092	11.8	8675	0.99	0.109	97.2
1.85-1.91	3.389	0.074	15.02	8510	0.993	0.088	98.5
1.91-1.98	3.331	0.056	19.7	8206	0.996	0.066	98.6
1.98-2.07	3.478	0.044	25.35	7878	0.997	0.052	98.3
2.07-2.16	3.378	0.037	29.54	7581	0.998	0.044	98.4
2.16-2.26	3.267	0.031	33.81	7250	0.998	0.037	98
2.26-2.39	3.322	0.027	38.73	6800	0.999	0.032	97.9
2.39-2.53	3.338	0.024	43.5	6505	0.999	0.029	97.5
2.53-2.7	3.347	0.021	48.44	6039	0.999	0.025	97.5
2.7-2.92	3.198	0.018	54.41	5665	0.999	0.022	97.2
2.92-3.2	3.201	0.016	60.98	5187	0.999	0.019	96.8
3.2-3.58	3.352	0.014	70.73	4667	0.999	0.017	96.7
3.58-4.13	3.215	0.013	74.02	4169	1	0.015	97.3
4.13-5.06	3.289	0.012	77.6	3554	1	0.014	97.9
5.06-7.16	3.351	0.012	75.44	2787	1	0.014	98.8
7.16-49.575	3.228	0.011	79.76	1551	1	0.013	97.9

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.14_3247	refinement
PDB_EXTRACT	3.24	data extraction
PHASER		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.6→49.575 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.34

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1755	1905	1.45 %	0
R_work	0.1494	-	-	-
obs	0.1498	131039	96.72 %	-

Solvent computation

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

Displacement parameters

B_iso max: 78.14 Å² / B_iso mean: 25.0433 Å² / B_iso min: 9.56 Å²

Refinement step

Cycle: final / Resolution: 1.6→49.575 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6701	0	204	1248	8153
B_iso mean	-	-	17.73	36.95	-
Num. residues	-	-	-	-	862

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7415
X-RAY DIFFRACTION	f_angle_d	0.978	10173
X-RAY DIFFRACTION	f_dihedral_angle_d	13.408	4641
X-RAY DIFFRACTION	f_chiral_restr	0.054	1117
X-RAY DIFFRACTION	f_plane_restr	0.006	1419

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.64	0.2512	122	0.1983	8455	8577	89
1.64-1.6844	0.2162	114	0.177	9025	9139	95
1.6844-1.7339	0.2108	144	0.1656	9075	9219	95
1.7339-1.7899	0.1865	159	0.1587	9110	9269	96
1.7899-1.8539	0.1995	117	0.1619	9257	9374	97
1.8539-1.9281	0.1823	146	0.1596	9399	9545	99
1.9281-2.0159	0.174	153	0.1594	9388	9541	99
2.0159-2.1221	0.1769	165	0.1535	9310	9475	98
2.1221-2.2551	0.1792	123	0.1505	9396	9519	98
2.2551-2.4292	0.1907	130	0.153	9312	9442	98
2.4292-2.6736	0.2264	142	0.1554	9325	9467	97
2.6736-3.0605	0.164	115	0.1521	9273	9388	97
3.0605-3.8557	0.1599	118	0.1363	9309	9427	97
3.8557-49.5988	0.1468	157	0.1373	9500	9657	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	3.134	0.4949	-0.9387	1.4334	-0.391	2.2521	-0.0491	0.1265	-0.1419	-0.0131	-0.0487	0.07	0.2771	-0.0474	0.0352	0.1882	0.0078	-0.0067	0.1252	-0.0097	0.107	45.8664	14.6099	-5.0316
2	0.9736	0.0666	-0.4632	1.9338	-1.2604	2.0398	-0.0028	0.0584	-0.2014	-0.0811	-0.064	0.1417	0.3522	0.0889	0.0952	0.2683	0.0334	0.0061	0.1356	-0.0332	0.175	49.3846	10.1065	-13.6008
3	1.9897	-1.7801	-0.3863	2.2994	0.1738	1.5557	-0.069	0.1591	-0.4224	-0.4276	-0.1233	-0.1916	0.5469	0.298	0.1236	0.3412	0.1023	0.0426	0.2057	-0.0023	0.2106	57.5917	14.5221	-24.9609
4	1.7106	-0.4418	-0.5281	4.1711	-0.5961	2.9006	0.0218	0.1316	0.0187	-0.777	-0.0642	0.1017	0.0734	0.1874	0.0225	0.2405	0.0177	-0.0299	0.167	-0.0001	0.1237	52.9835	27.7511	-26.8781
5	1.0718	0.5421	-0.2631	2.3719	-0.5206	2.0505	0.0233	-0.0223	0.0259	-0.243	-0.0704	0.1262	0.0758	0.1113	-0.0105	0.1635	0.0191	-0.0182	0.1372	-0.0074	0.17	50.0697	27.1918	-19.3833
6	1.4673	1.0416	-0.51	2.5034	-0.6119	2.0187	-0.0045	0.1289	0.0736	0.0042	0.0557	0.2506	0.1317	-0.0954	0.0019	0.159	-0.0019	-0.0131	0.1601	0.0089	0.1645	46.2474	23.4578	-10.1106
7	5.177	-1.8044	0.5472	3.8443	-1.1166	2.947	-0.0537	0.0448	0.3627	0.1149	0.0593	0.2911	-0.0577	-0.0092	0.0224	0.1445	0.004	-0.0022	0.1216	0.0182	0.1967	49.136	21.8789	-4.196
8	1.696	0.3829	-0.6659	1.6752	-0.6379	2.048	-0.0112	-0.0684	-0.0431	-0.0475	-0.1432	-0.2839	0.1018	0.5247	0.1484	0.1546	0.0492	-0.0232	0.2865	0.0342	0.1766	65.0696	19.116	-6.8697
9	2.2963	0.1668	-0.177	1.8839	-0.4699	2.604	-0.1529	-0.186	-0.2964	0.0438	-0.0685	-0.1086	0.3961	0.0924	0.0909	0.2198	0.0261	0.0342	0.1426	0.0165	0.1875	48.3581	8.4052	0.6526
10	4.8267	2.7078	-1.2457	2.2436	-1.0827	0.9262	0.1855	-0.5429	0.1137	0.1145	-0.3203	-0.127	-0.0587	0.5667	0.1857	0.1912	0.0011	-0.0163	0.4741	0.0222	0.2051	67.0029	19.1797	1.7906
11	2.4424	-0.0186	0.7011	0.8744	0.1086	1.717	-0.0542	0.1533	0.1631	-0.0144	0.0167	-0.0669	-0.2527	0.1161	0.0197	0.1706	-0.0421	0.0056	0.1492	0.0074	0.1278	37.2325	60.928	37.4369
12	0.9077	0.4222	0.8761	2.3788	1.8191	2.9164	-0.0295	0.1541	0.138	-0.1158	0.0235	-0.0851	-0.4119	0.2371	-0.0496	0.2236	-0.0658	0.0038	0.1727	0.0143	0.1601	39.656	59.8677	29.262
13	2.2314	-1.3853	0.1332	2.8727	0.1434	2.6166	0.0354	0.142	0.2239	-0.2441	-0.0356	0.1085	-0.4271	-0.1747	0.057	0.226	0.0174	-0.013	0.1574	0.0089	0.2127	28.7906	57.8952	19.9579
14	1.3568	-0.9903	0.3043	3.4532	0.3276	2.274	0.0484	0.1213	-0.0659	-0.5185	-0.0751	0.0281	0.0055	-0.0466	-0.0174	0.1789	-0.0132	0.013	0.1749	-0.01	0.1472	33.6339	45.2051	18.1657
15	0.5207	-0.268	-0.0008	1.744	0.5122	2.0794	-0.014	-0.0025	0.0526	-0.072	-0.0252	-0.014	-0.0662	0.0841	-0.0379	0.1184	-0.0228	0.0025	0.1278	0.0006	0.1633	36.4928	45.9225	25.6996
16	0.9229	0.3338	0.4365	2.3207	0.523	1.946	-0.0198	0.1725	-0.0164	0.0047	0.1445	-0.1238	-0.0451	0.1651	-0.0391	0.1365	-0.0314	0.0034	0.1744	-0.0172	0.1396	39.3343	48.9095	35.2642
17	6.1633	-2.4016	-1.0215	3.1692	1.0356	2.376	-0.2075	0.2049	-0.3201	0.1518	0.127	-0.2186	0.0987	0.1329	-0.0319	0.1425	-0.0431	0.0096	0.1489	-0.011	0.1826	37.2227	51.1416	40.8053
18	1.563	-0.0738	0.266	1.7863	0.2556	3.8739	-0.0507	0.1345	0.1104	-0.2551	0.0758	0.3183	-0.172	-0.5766	0.164	0.1884	0.0103	-0.0384	0.2611	-0.0092	0.2085	16.2088	58.2253	33.2915
19	1.5387	0.6334	1.0365	1.4552	0.3987	2.6259	0.051	-0.0609	-0.0882	0.0578	-0.1147	0.1187	0.1677	-0.2943	0.0285	0.1631	-0.0249	0.0372	0.2223	-0.0081	0.1803	23.1704	50.8303	40.4255
20	2.1068	-0.2989	0.254	1.3937	0.2772	1.9734	-0.1185	-0.0438	0.2206	0.155	0.013	0.0143	-0.2253	0.0908	0.0262	0.2097	-0.0315	-0.0095	0.1423	-0.0155	0.1651	37.7029	64.2382	46.0643
21	3.7172	1.9146	0.1195	2.2851	0.3935	1.5353	0.1361	-0.2152	-0.1759	0.1766	-0.146	0.2068	0.1784	-0.4109	0.0649	0.1983	-0.0307	0.0252	0.2986	-0.0059	0.2005	19.1617	53.0224	47.0043
22	2.4435	-0.7532	-0.4594	1.732	0.4995	1.9062	-0.0699	0.0322	-0.1225	0.001	0.0812	-0.0811	0.2533	0.2396	-0.0417	0.1655	0.0282	-0.0076	0.151	-0.0136	0.1307	33.3682	16.2477	14.678
23	0.3552	0.1888	0.0622	1.4665	0.3481	1.2783	0.0124	-0.0538	-0.0335	0.1271	0.0093	-0.0656	0.098	0.1094	-0.0369	0.1215	0.0199	-0.0084	0.1294	0.0056	0.1483	31.0086	24.5799	27.4523
24	1.4473	-0.0779	-0.2506	2.0893	0.4084	1.6853	-0.0226	0.0448	0.0909	-0.0554	0.0062	0.1065	-0.095	-0.1029	0.0321	0.1301	0.0158	-0.0398	0.1181	0.0152	0.1514	21.0368	27.3528	15.6567
25	1.9325	-0.4103	-0.1202	1.686	0.2511	2.082	0.0565	0.2437	-0.1271	-0.2377	-0.0994	0.2194	-0.0489	-0.1296	0.0074	0.2026	0.0279	-0.0307	0.1641	-0.0132	0.1603	23.2041	18.9523	8.2687
26	2.8288	-1.2772	0.2367	2.3249	-0.4654	2.1789	0.0998	0.0978	0.1146	-0.0001	-0.0714	0.0054	-0.2609	0.1175	-0.0418	0.173	-0.035	0.0252	0.1414	0.0052	0.1329	54.6554	55.548	-29.7285
27	0.5758	0.1437	-0.329	2.0126	-0.6987	1.5323	0.0654	-0.1209	0.098	0.2359	-0.0833	-0.1004	-0.1967	0.3777	0.0027	0.1432	-0.0575	-0.0134	0.1784	-0.0221	0.141	58.1592	48.9553	-15.1753
28	1.3436	-0.8385	-0.1096	2.9702	-0.8384	1.9102	0.0207	-0.0377	0.003	0.0802	0.0692	0.1492	-0.0539	0.1196	-0.0502	0.1348	-0.0206	0.0016	0.1371	0.0028	0.1392	51.9465	47.2668	-25.0262
29	1.1212	-0.1811	0.3386	2.4553	-0.3774	2.1347	-0.0089	-0.0288	-0.0259	0.0626	-0.0007	-0.1681	0.0181	0.3556	0.0747	0.1694	0.0031	0.0325	0.1996	0.0155	0.1819	65.6488	48.1029	-27.4581
30	2.319	-0.8455	1.7487	2.1891	-1.4992	4.8252	0.1623	-0.0554	-0.3292	-0.134	-0.0415	-0.3261	0.618	0.3092	0.0208	0.2616	0.0439	0.0465	0.2808	-0.0224	0.2789	69.311	38.4301	-27.9847
31	1.8978	-0.422	-0.1018	2.0672	-0.2911	2.1385	0.0388	0.2258	0.044	-0.1605	-0.1658	-0.3118	0.0744	0.3904	0.0401	0.188	-0.017	0.026	0.2355	0.02	0.1668	64.2885	53.1427	-36.4359

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 2 through 23 )	A	2 - 23
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 46 )	A	24 - 46
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 59 )	A	47 - 59
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 60 through 73 )	A	60 - 73
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 74 through 98 )	A	74 - 98
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 99 through 121 )	A	99 - 121
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 122 through 137 )	A	122 - 137
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 138 through 183 )	A	138 - 183
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 184 through 203 )	A	184 - 203
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 204 through 217 )	A	204 - 217
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 3 through 34 )	B	3 - 34
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 35 through 46 )	B	35 - 46
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 47 through 59 )	B	47 - 59
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 60 through 73 )	B	60 - 73
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 74 through 98 )	B	74 - 98
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 99 through 121 )	B	99 - 121
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 122 through 137 )	B	122 - 137
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 138 through 152 )	B	138 - 152
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 153 through 183 )	B	153 - 183
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 184 through 203 )	B	184 - 203
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 204 through 217 )	B	204 - 217
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 2 through 23 )	C	2 - 23
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 24 through 121 )	C	24 - 121
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 122 through 183 )	C	122 - 183
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 184 through 217 )	C	184 - 217
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 3 through 23 )	D	3 - 23
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 24 through 98 )	D	24 - 98
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 99 through 121 )	D	99 - 121
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 122 through 152 )	D	122 - 152
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 153 through 172 )	D	153 - 172
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 173 through 217 )	D	173 - 217

-
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