PDB-2fvk: Crystal structure of dihydropyrimidinase from Saccharomyces kluyv...

ID or keywords:

Entry

Database: PDB / ID: 2fvk

Title

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

Components

dihydropyrimidinase

Keywords

HYDROLASE / beta/alpha barrel / beta sandwich

Function / homology

Function and homology information

dihydropyrimidinase / dihydropyrimidinase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Lachancea kluyveri (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.4 Å

Authors

Dobritzsch, D. / Lohkamp, B.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: The Crystal Structures of Dihydropyrimidinases Reaffirm the Close Relationship between Cyclic Amidohydrolases and Explain Their Substrate Specificity.
Authors: Lohkamp, B. / Andersen, B. / Piskur, J. / Dobritzsch, D.

History

Deposition	Jan 31, 2006	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 14, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 25, 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2fvk.cif.gz	427.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2fvk.ent.gz	349.5 KB	Display	PDB format
PDBx/mmJSON format	2fvk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fv/2fvk ftp://data.pdbj.org/pub/pdb/validation_reports/fv/2fvk	HTTPS FTP

-
Related structure data

Related structure data	2ftwC 2ftySC 2fvmC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2fty-d 2fvm-d 3gli-1 6uen-d 1gkq-d 4v1t-d 6ddb-1 6ddc-1 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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4)

Deposited unit

A: dihydropyrimidinase

B: dihydropyrimidinase

C: dihydropyrimidinase

D: dihydropyrimidinase

hetero molecules

250 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)	90.130, 71.600, 161.890
Angle α, β, γ (deg.)	90.00, 91.40, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ILE	ILE	SER	SER	2	A	A	3 - 103	2 - 102
2	1	ILE	ILE	SER	SER	2	B	B	3 - 103	2 - 102
3	1	ILE	ILE	SER	SER	2	C	C	3 - 103	2 - 102
4	1	ILE	ILE	SER	SER	2	D	D	3 - 103	2 - 102
5	2	GLY	GLY	GLU	GLU	2	A	A	106 - 140	105 - 139
6	2	GLY	GLY	GLU	GLU	2	B	B	106 - 140	105 - 139
7	2	GLY	GLY	GLU	GLU	2	C	C	106 - 140	105 - 139
8	2	GLY	GLY	GLU	GLU	2	D	D	106 - 140	105 - 139
9	3	VAL	VAL	THR	THR	2	A	A	152 - 171	151 - 170
10	3	VAL	VAL	THR	THR	2	B	B	152 - 171	151 - 170
11	3	VAL	VAL	THR	THR	2	C	C	152 - 171	151 - 170
12	3	VAL	VAL	THR	THR	2	D	D	152 - 171	151 - 170
13	4	ILE	ILE	PRO	PRO	2	A	A	306 - 379	305 - 378
14	4	ILE	ILE	PRO	PRO	2	B	B	306 - 379	305 - 378
15	4	ILE	ILE	PRO	PRO	2	C	C	306 - 379	305 - 378
16	4	ILE	ILE	PRO	PRO	2	D	D	306 - 379	305 - 378
17	5	ASN	ASN	TYR	TYR	2	A	A	382 - 540	381 - 539
18	5	ASN	ASN	TYR	TYR	2	B	B	382 - 540	381 - 539
19	5	ASN	ASN	TYR	TYR	2	C	C	382 - 540	381 - 539
20	5	ASN	ASN	TYR	TYR	2	D	D	382 - 540	381 - 539
21	6	PRO	PRO	ARG	ARG	2	A	A	173 - 292	172 - 291
22	6	PRO	PRO	ARG	ARG	2	B	B	173 - 292	172 - 291
23	6	PRO	PRO	ARG	ARG	2	C	C	173 - 292	172 - 291
24	6	PRO	PRO	ARG	ARG	2	D	D	173 - 292	172 - 291
25	7	ZN	ZN	DUC	DUC	6	A	E - G	601 - 604
26	7	ZN	ZN	DUC	DUC	6	B	H - J	601 - 604
27	7	ZN	ZN	DUC	DUC	6	C	K - M	601 - 604
28	7	ZN	ZN	DUC	DUC	6	D	N - P	601 - 604

Details

the content of the asymmetric unit equals the biological assembly, which is a homotetramer

#1: Protein	dihydropyrimidinase Mass: 62325.090 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachancea kluyveri (fungus) / Gene: Pyd2 / Plasmid: P343 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9P903, dihydropyrimidinase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-DUC / DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / DIHYDROURACIL Mass: 114.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆N₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1043 / 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: 2.09 Å³/Da / Density % sol: 41.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.1M ammonium sulfate, 1mM CaCl2, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Feb 8, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 2.4→54.23 Å / Num. all: 80380 / Num. obs: 80380 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / B_iso Wilson estimate: 43.1 Å² / R_sym value: 0.097 / Net I/σ(I): 11
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 11234 / R_sym value: 0.329 / % possible all: 95.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB entry 2fty

2fty

Resolution: 2.4→54.23 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.916 / SU B: 16.32 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.782 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23352	4085	5.1 %	RANDOM
R_work	0.17784	-	-	-
obs	0.18064	80363	99.14 %	-
all	-	80363	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 34.204 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.9 Å²	0 Å²	-1.87 Å²
2-	-	2.76 Å²	0 Å²
3-	-	-	-1.96 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→54.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16594	0	40	1043	17677

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	17056
X-RAY DIFFRACTION	r_angle_refined_deg	1.179	1.968	23113
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.885	5	2129
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.861	24.986	726
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.297	15	2909
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.567	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	2561
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	12828
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	8510
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	11663
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	1330
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.238	0.2	50
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.157	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.257	1.5	10877
X-RAY DIFFRACTION	r_mcangle_it	0.458	2	17189
X-RAY DIFFRACTION	r_scbond_it	1.013	3	7065
X-RAY DIFFRACTION	r_scangle_it	1.508	4.5	5919

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2033	tight positional	0.03	0.05
2	B	2033	tight positional	0.03	0.05
3	C	2033	tight positional	0.03	0.05
4	D	2033	tight positional	0.03	0.05
1	A	1929	medium positional	0.3	0.5
2	B	1929	medium positional	0.35	0.5
3	C	1929	medium positional	0.39	0.5
4	D	1929	medium positional	0.36	0.5
1	A	10	loose positional	0.17	5
2	B	10	loose positional	0.29	5
3	C	10	loose positional	0.25	5
4	D	10	loose positional	0.25	5
1	A	2033	tight thermal	0.05	0.5
2	B	2033	tight thermal	0.05	0.5
3	C	2033	tight thermal	0.05	0.5
4	D	2033	tight thermal	0.05	0.5
1	A	1929	medium thermal	0.36	2
2	B	1929	medium thermal	0.35	2
3	C	1929	medium thermal	0.36	2
4	D	1929	medium thermal	0.33	2
1	A	10	loose thermal	1.78	10
2	B	10	loose thermal	1.59	10
3	C	10	loose thermal	1.65	10
4	D	10	loose thermal	1.28	10

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	288	-
R_work	0.26	5185	-
obs	-	-	92.67 %

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	1.7128	-0.0384	0.3514	0.7247	-0.0374	1.0632	0.0113	-0.2438	-0.0774	0.1192	-0.0468	0.1172	0.1633	-0.2684	0.0355	-0.0572	-0.0432	0.0709	-0.1202	-0.0038	-0.0652	46.2445	54.5945	76.2517
2	4.2511	0.5257	0.2244	2.8482	0.737	5.9458	-0.1266	0.5087	0.5566	-0.1916	0.0759	0.4549	-0.2942	-0.2169	0.0506	-0.0872	-0.0084	0.025	-0.0466	0.0035	0.0468	34.5507	70.096	59.3064
3	0.6728	-0.1059	0.0422	0.9092	0.4635	1.0006	0.0089	0.0535	-0.0437	0.03	-0.0696	0.2443	0.0967	-0.1776	0.0606	-0.0971	-0.0247	0.0049	-0.1149	-0.0011	-0.0817	43.2314	54.9883	47.775
4	1.8763	2.04	0.2273	6.9937	-1.2688	1.9451	-0.0148	0.1599	-0.2758	-0.2902	-0.0186	-0.1679	0.4503	0.1592	0.0334	-0.0951	0.0381	0.0157	-0.108	-0.0362	-0.1042	55.6001	49.3122	53.5317
5	1.2293	0.3985	0.3083	0.9867	0.1877	1.6573	0.0727	-0.045	-0.2756	0.0351	-0.0308	0.0106	0.3417	-0.085	-0.0418	-0.0043	-0.0188	0.0268	-0.1641	0.04	-0.033	50.7857	42.4128	67.6789
6	1.663	1.2277	-0.7738	2.8187	-3.6497	7.7965	0.0641	0.0249	0.1506	0.2001	-0.15	0.1271	-0.6847	0.0195	0.0859	-0.0497	0.0457	0.0199	-0.1772	-0.0526	-0.0199	47.1275	72.409	59.6299
7	1.2216	0.0589	0.0285	0.7077	-0.1517	1.1243	-0.0055	0.2325	0.1034	-0.1094	0.0158	0.0823	-0.1296	-0.164	-0.0103	-0.0502	0.0253	-0.0413	-0.0828	0.0079	-0.0947	49.7943	63.413	3.302
8	1.8141	0.4289	-0.9263	2.4628	-0.9775	4.1199	-0.0833	-0.0468	-0.2278	0.0407	0.0962	0.2978	0.3329	-0.4006	-0.0129	-0.1369	0.0646	-0.0447	0.0257	-0.013	0.0061	35.9412	54.7345	18.0703
9	0.7147	0.0296	-0.1451	0.4518	0.2503	0.9023	0.0007	-0.0641	0.0134	-0.0234	-0.0323	0.1596	-0.106	-0.1803	0.0317	-0.0945	0.0321	-0.0017	-0.0998	0.0094	-0.0852	42.805	60.7151	29.9683
10	1.922	-1.5682	-0.4373	8.5956	-1.4231	2.6174	0.0012	-0.0246	0.2134	0.3879	-0.042	-0.045	-0.4884	0.0688	0.0408	-0.0935	-0.0288	0.0003	-0.1071	-0.0357	-0.1321	56.2458	68.4661	27.6776
11	1.2733	-0.4945	-0.2828	0.9953	0.2478	1.5856	0.0301	0.0417	0.2525	-0.0313	0.0024	-0.0021	-0.3547	-0.0397	-0.0324	-0.0046	0.0042	-0.0194	-0.127	0.0394	-0.0473	52.2086	75.3508	13.2803
12	1.1914	-0.7857	0.472	3.3776	-3.884	6.9887	0.1391	0.0704	-0.2416	-0.0825	-0.101	0.2795	0.513	0.1339	-0.0381	-0.0569	-0.0052	-0.0067	-0.1073	-0.066	-0.0405	48.2582	45.3218	21.1073
13	2.2639	-0.1848	-0.4598	0.9699	0.2231	1.1072	0.0068	-0.2071	0.0627	0.0646	0.0455	-0.1341	-0.0916	0.2666	-0.0523	-0.0575	-0.0488	-0.0386	-0.1054	0.003	-0.1126	85.3868	68.9865	73.7805
14	0.9121	-0.097	-0.1403	0.1584	0.0126	1.3615	0.0501	0.082	0.0492	0.0102	0.0043	-0.1847	-0.2095	0.2562	-0.0544	-0.0775	-0.0496	0.0132	-0.0995	-0.0064	-0.079	89.4144	63.1442	51.0396
15	2.2685	2.3145	-0.4	8.7007	-0.2656	2.4871	0.0025	0.2323	0.2156	-0.406	-0.0317	0.1212	-0.4684	-0.0196	0.0292	-0.0673	0.0157	0.0069	-0.1032	0.0267	-0.1388	75.7976	70.4424	51.9383
16	1.9697	0.9044	-0.1916	2.1165	0.146	2.0219	0.0566	0.3022	0.5338	-0.2819	0.0034	0.0536	-0.6095	0.199	-0.06	0.1623	-0.0527	0.0511	-0.0929	0.0628	0.0503	84.2255	83.4602	54.0866
17	1.1928	0.0502	-0.1397	1.2515	0.2976	1.5474	0.0231	0.0612	0.1032	-0.0393	-0.0114	-0.0973	-0.2379	0.0625	-0.0116	-0.0505	-0.0428	0.0014	-0.166	0.022	-0.0962	77.9177	74.267	65.8701
18	0.8681	-0.135	-0.2738	1.8984	0.7647	1.9024	-0.0016	-0.1349	0.1138	0.0953	0.0314	0.076	-0.2344	0.1122	-0.0298	-0.1269	-0.0439	0.0038	-0.1297	0.0213	-0.0556	79.583	74.1372	70.4858
19	2.0366	0.0499	0.791	0.7392	0.2301	1.4134	0.0662	0.2964	-0.1277	-0.0899	0.025	-0.1134	0.1949	0.2986	-0.0913	-0.0369	0.0702	0.0217	-0.0004	-0.0179	-0.0795	84.992	46.5254	5.9512
20	0.9099	-0.7537	0.1709	2.3606	0.3377	2.1275	-0.1119	-0.0085	0.3137	-0.0705	0.1264	-0.4842	-0.4819	0.4591	-0.0145	-0.0985	-0.0116	0.0157	0.1274	-0.0426	0.0508	97.1439	59.6508	21.2095
21	0.7706	-0.0039	-0.0109	0.4253	-0.0937	1.7146	-0.0046	-0.0305	-0.0212	0.0016	-0.0524	-0.1788	0.1176	0.2137	0.057	-0.1084	0.0229	-0.0135	-0.0443	-0.0139	-0.0789	90.131	55.1505	31.6817
22	2.224	-2.595	0.281	11.1774	0.6978	2.1951	0.0268	-0.175	-0.3117	0.5961	-0.1258	0.1367	0.3705	0.0343	0.099	-0.0938	-0.0128	-0.0124	-0.0375	0.0205	-0.0967	76.8352	47.0107	30.5576
23	1.3955	-0.3632	0.4361	0.9408	0.1762	2.2555	0.0811	-0.081	-0.3044	0.0822	0.0161	-0.0689	0.4627	0.104	-0.0972	0.0366	0.0276	-0.0342	-0.0954	-0.0017	-0.0138	81.6097	37.1054	18.0136
24	0.9454	-1.1499	-1.151	5.1877	5.0538	6.4897	0.0622	0.1325	0.2459	-0.2864	-0.0974	-0.0123	-0.5973	0.0449	0.0352	-0.0125	-0.02	-0.0039	-0.0238	0.0558	-0.0376	85.0116	69.2503	20.3402

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 139	1 - 138
2	X-RAY DIFFRACTION	2	A	A	140 - 167	139 - 166
3	X-RAY DIFFRACTION	3	A	A	168 - 254	167 - 253
4	X-RAY DIFFRACTION	4	A	A	255 - 306	254 - 305
5	X-RAY DIFFRACTION	5	A	A	307 - 513	306 - 512
6	X-RAY DIFFRACTION	6	A	A	514 - 541	513 - 540
7	X-RAY DIFFRACTION	7	B	B	2 - 122	1 - 121
8	X-RAY DIFFRACTION	8	B	B	123 - 151	122 - 150
9	X-RAY DIFFRACTION	9	B	B	152 - 254	151 - 253
10	X-RAY DIFFRACTION	10	B	B	255 - 306	254 - 305
11	X-RAY DIFFRACTION	11	B	B	307 - 513	306 - 512
12	X-RAY DIFFRACTION	12	B	B	514 - 541	513 - 540
13	X-RAY DIFFRACTION	13	C	C	2 - 151	1 - 150
14	X-RAY DIFFRACTION	14	C	C	152 - 254	151 - 253
15	X-RAY DIFFRACTION	15	C	C	255 - 306	254 - 305
16	X-RAY DIFFRACTION	16	C	C	307 - 379	306 - 378
17	X-RAY DIFFRACTION	17	C	C	380 - 455	379 - 454
18	X-RAY DIFFRACTION	18	C	C	456 - 541	455 - 540
19	X-RAY DIFFRACTION	19	D	D	2 - 125	1 - 124
20	X-RAY DIFFRACTION	20	D	D	126 - 150	125 - 149
21	X-RAY DIFFRACTION	21	D	D	151 - 254	150 - 253
22	X-RAY DIFFRACTION	22	D	D	255 - 306	254 - 305
23	X-RAY DIFFRACTION	23	D	D	307 - 514	306 - 513
24	X-RAY DIFFRACTION	24	D	D	515 - 542	514 - 541

-
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