PDB-7v4z: Structure of Horcolin native form

ID or keywords:

Entry

Database: PDB / ID: 7v4z

Title

Structure of Horcolin native form

Components

Horcolin

Keywords

SUGAR BINDING PROTEIN / Horcolin / mannose-binding lectin

Function / homology

Function and homology information

apoplast / D-mannose binding
Similarity search - Function

Biological species

Hordeum vulgare (barley)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.16 Å

Authors

Bobbili, K.B. / Sivaji, N. / Jayaprakash, N.G. / Narayanan, V. / Sekhar, A. / Suguna, K. / Surolia, A.

Funding support

India, 1items

Citation

Journal: Biochemistry / Year: 2022
Title: Structure and Carbohydrate Recognition by the Nonmitogenic Lectin Horcolin.
Authors: Narayanan, V. / Bobbili, K.B. / Sivaji, N. / Jayaprakash, N.G. / Suguna, K. / Surolia, A. / Sekhar, A.

History

Deposition	Aug 16, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 30, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7v4z.cif.gz	597.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7v4z.ent.gz	480.3 KB	Display	PDB format
PDBx/mmJSON format	7v4z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7v4z_validation.pdf.gz	550.5 KB	Display	wwPDB validaton report
Full document	7v4z_full_validation.pdf.gz	563.3 KB	Display
Data in XML	7v4z_validation.xml.gz	75.1 KB	Display
Data in CIF	7v4z_validation.cif.gz	107.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/7v4z ftp://data.pdbj.org/pub/pdb/validation_reports/v4/7v4z	HTTPS FTP

-
Related structure data

Related structure data	7v4sC 1x1vS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7v4z-5 7v4z-3 7v4z-6 5xe8-d 3qgy-1 7kmv-6 1sm2-2 7v4z-2 5p9l-d 6sj5-2 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) 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

7v4sC

1x1vS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Horcolin

C: Horcolin

B: Horcolin

D: Horcolin

E: Horcolin

F: Horcolin

G: Horcolin

H: Horcolin

I: Horcolin

J: Horcolin

K: Horcolin

L: Horcolin

hetero molecules

184 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Horcolin

C: Horcolin

hetero molecules

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

2

B: Horcolin

D: Horcolin

hetero molecules

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

3

E: Horcolin

F: Horcolin

hetero molecules

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

4

G: Horcolin

H: Horcolin

hetero molecules

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

5

I: Horcolin

J: Horcolin

hetero molecules

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

6

K: Horcolin

L: Horcolin

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.179, 94.419, 238.359
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

#1: Protein	Horcolin / Agglutinin / Mannose-specific lectin Mass: 15136.077 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q5U9T2
#2: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1358 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.15 %
Crystal grow	Temperature: 293 K / Method: microbatch Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.16→59.83 Å / Num. obs: 513816 / % possible obs: 96.8 % / Redundancy: 5.1 % / CC_1/2: 0.99 / R_merge(I) obs: 0.092 / Net I/σ(I): 8.9
Reflection shell	Resolution: 1.16→1.23 Å / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 69425 / CC_1/2: 0.876

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1X1V

1x1v

Resolution: 1.16→55.866 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.959 / SU B: 1.383 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1962	25278	4.921 %
R_work	0.1815	488415	-
all	0.182	-	-
obs	-	513693	96.663 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 14.413 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.228 Å²	0 Å²	0 Å²
2-	-	0.246 Å²	-0 Å²
3-	-	-	-0.475 Å²

Refinement step

Cycle: LAST / Resolution: 1.16→55.866 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12444	0	179	1358	13981

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.013	12856
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	12018
X-RAY DIFFRACTION	r_angle_refined_deg	1.974	1.645	17410
X-RAY DIFFRACTION	r_angle_other_deg	1.573	1.579	27789
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.071	5	1709
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.264	21.983	484
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.545	15	1879
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.971	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1781
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	14481
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2688
X-RAY DIFFRACTION	r_nbd_refined	0.162	0.2	1721
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	11308
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	6612
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.101	0.2	6755
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	803
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.138	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.28	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	100
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.149	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	0.731	0.599	6872
X-RAY DIFFRACTION	r_mcbond_other	0.729	0.599	6871
X-RAY DIFFRACTION	r_mcangle_it	1.083	0.902	8569
X-RAY DIFFRACTION	r_mcangle_other	1.084	0.902	8570
X-RAY DIFFRACTION	r_scbond_it	1.302	0.752	5984
X-RAY DIFFRACTION	r_scbond_other	1.302	0.752	5985
X-RAY DIFFRACTION	r_scangle_it	1.927	1.067	8841
X-RAY DIFFRACTION	r_scangle_other	1.927	1.067	8842
X-RAY DIFFRACTION	r_lrange_it	4.432	8.435	13508
X-RAY DIFFRACTION	r_lrange_other	4.431	8.437	13509
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	4181
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.059	0.05	4284
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.106	0.05	4187
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.057	0.05	4310
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.098	0.05	4143
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.108	0.05	4179
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.072	0.05	4259
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.096	0.05	4181
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.073	0.05	4231
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.103	0.05	4154
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.06	0.05	4272
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.1	0.05	4122
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.062	0.05	4358
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.1	0.05	4164
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.067	0.05	4298
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.093	0.05	4290
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.101	0.05	4197
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.079	0.05	4262
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.094	0.05	4215
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.091	0.05	4248
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.094	0.05	4199
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.096	0.05	4153
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.058	0.05	4312
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.09	0.05	4170
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.1	0.05	4146
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.066	0.05	4269
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.088	0.05	4215
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.063	0.05	4200
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.097	0.05	4184
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.065	0.05	4263
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.107	0.05	4174
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.061	0.05	4313
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.078	0.05	4368
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.103	0.05	4217
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.071	0.05	4314
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.094	0.05	4242
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.081	0.05	4299
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.102	0.05	4211
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.098	0.05	4182
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.104	0.05	4171
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.074	0.05	4295
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.097	0.05	4238
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.074	0.05	4210
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.1	0.05	4207
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.061	0.05	4307
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.081	0.05	4278
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.098	0.05	4221
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.074	0.05	4310
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.09	0.05	4196
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.081	0.05	4299
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.096	0.05	4221
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.103	0.05	4204
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.065	0.05	4333
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.091	0.05	4250
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.048	0.05	4360
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.102	0.05	4212
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.097	0.05	4277
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.069	0.05	4261
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.105	0.05	4248
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.051	0.05	4414
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.09	0.05	4207
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.061	0.05	4380
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.093	0.05	4276
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.087	0.05	4209
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.055	0.05	4279
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.101	0.05	4249

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 (%)
1.2-1.21	0.235	1705	0.234	32845	X-RAY DIFFRACTION	88.3496
1.226-1.261	0.243	1682	0.24	33186	X-RAY DIFFRACTION	94.1742
1.261-1.3	0.242	1695	0.235	32480	X-RAY DIFFRACTION	95.015
1.3-1.343	0.239	1644	0.224	31703	X-RAY DIFFRACTION	95.6241
1.343-1.39	0.2	1600	0.193	30674	X-RAY DIFFRACTION	95.6749
1.39-1.442	0.222	1548	0.208	29975	X-RAY DIFFRACTION	96.5897
1.442-1.501	0.211	1468	0.195	29180	X-RAY DIFFRACTION	97.658
1.501-1.568	0.199	1434	0.187	28180	X-RAY DIFFRACTION	98.4737
1.568-1.645	0.18	1348	0.165	27059	X-RAY DIFFRACTION	98.5089
1.645-1.734	0.192	1379	0.181	25781	X-RAY DIFFRACTION	98.994
1.734-1.839	0.194	1253	0.173	24674	X-RAY DIFFRACTION	99.8844
1.839-1.966	0.185	1208	0.166	23262	X-RAY DIFFRACTION	99.9428
1.966-2.123	0.174	1065	0.16	21728	X-RAY DIFFRACTION	99.943
2.123-2.326	0.174	1089	0.164	19941	X-RAY DIFFRACTION	99.9572
2.326-2.6	0.187	926	0.171	18153	X-RAY DIFFRACTION	99.9948
2.6-3.002	0.185	876	0.174	16058	X-RAY DIFFRACTION	99.9882
3.002-3.676	0.189	775	0.168	13578	X-RAY DIFFRACTION	99.9652
3.676-5.196	0.18	528	0.166	10705	X-RAY DIFFRACTION	99.8134
5.196-55.86	0.265	323	0.226	6124	X-RAY DIFFRACTION	99.8142

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	1.0381	0.1049	-0.245	0.8744	-0.045	1.4155	0.0176	0.0081	0.0651	0.0332	-0.0317	-0.053	-0.0469	0.1181	0.014	0.0298	-0.0095	-0.0017	0.0254	-0.0029	0.041	31.4273	15.5408	35.0863
2	1.1066	0.5762	-0.0728	1.6601	0.1949	1.833	-0.0138	0.1312	0.0668	-0.0787	-0.016	0.1064	0.0851	-0.0113	0.0298	0.0335	0.0035	-0.0064	0.0395	-0.002	0.0316	24.7893	3.0501	14.2464
3	0.7861	-0.0347	0.5681	1.2231	0.1806	3.5002	0.0582	0.046	-0.0969	-0.0059	0.0587	-0.1192	0.3372	0.4951	-0.1169	0.0798	0.0631	-0.0106	0.0996	-0.0309	0.0623	30.9125	-14.7725	44.6441
4	0.9828	-0.5528	0.3957	1.4459	-0.5663	2.6191	0.0052	-0.0864	-0.0557	0.096	0.0026	0.04	-0.067	0.1176	-0.0078	0.0238	-0.0103	0.0045	0.0427	0.0023	0.033	22.9362	-2.6003	65.1286
5	0.9457	-0.39	-0.0272	1.4188	-0.2961	2.1675	-0.0238	-0.0166	0.0209	-0.0026	0.0691	0.078	-0.0491	-0.2545	-0.0453	0.0303	0.0133	0.0041	0.0465	0.023	0.0442	40.2902	-31.8717	4.0439
6	1.0655	-0.5032	-0.1641	1.6688	-0.3959	2.1063	-0.0038	-0.1324	0.0587	0.0776	0.0633	-0.0877	0.0019	-0.1596	-0.0595	0.0303	0.0068	-0.0115	0.0643	0.0209	0.0444	46.9442	-43.3503	25.4642
7	0.8508	-0.1779	0.3434	1.2984	-0.2054	1.3783	0.0515	-0.005	-0.0172	0.0299	-0.0275	-0.0646	-0.1442	0.0185	-0.024	0.0485	0.0045	0.0029	0.0082	-0.015	0.0717	7.9824	-29.6956	18.9079
8	0.8656	0.2933	0.2646	2.2394	0.5882	1.6961	0.0096	0.0041	-0.0606	-0.0196	0.0791	-0.2866	0.0349	0.0973	-0.0888	0.0265	-0.0006	0.0012	0.007	-0.0099	0.092	15.2352	-53.4544	14.4676
9	1.0739	0.1834	-1.0546	1.5595	-0.4507	2.4386	-0.0057	-0.0003	0.0214	-0.0216	-0.0035	-0.006	0.1665	0.017	0.0092	0.0404	-0.0035	-0.002	0.0213	0.0259	0.0847	62.5493	-16.6402	60.0391
10	1.1099	0.1984	-0.3319	1.7928	-0.5287	1.9266	0.0292	-0.0059	0.0905	0.1394	0.1253	0.2527	-0.1787	-0.195	-0.1545	0.0931	0.0341	0.0444	0.0429	0.0445	0.114	55.1828	6.9487	55.6727
11	0.9727	0.1563	0.4014	1.4676	-0.0865	1.3939	0.0339	0.0168	-0.0352	0.0366	-0.0186	0.0689	-0.0676	0.0176	-0.0153	0.0225	-0.0046	0.0016	0.0052	0.013	0.0721	63.5536	17.5771	22.0854
12	0.9693	-0.4225	0.2726	1.8719	-0.4191	1.5534	0.0037	-0.0081	-0.0768	-0.0479	0.0558	0.2056	0.0469	-0.0839	-0.0595	0.05	-0.0031	0.0001	0.0055	0.0089	0.0783	56.1027	-6.1447	26.0836

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 204
2	X-RAY DIFFRACTION	2	ALL	C	3 - 304
3	X-RAY DIFFRACTION	3	ALL	B	4 - 301
4	X-RAY DIFFRACTION	4	ALL	D	3 - 303
5	X-RAY DIFFRACTION	5	ALL	E	4 - 302
6	X-RAY DIFFRACTION	6	ALL	F	4 - 301
7	X-RAY DIFFRACTION	7	ALL	G	3 - 305
8	X-RAY DIFFRACTION	8	ALL	H	4 - 302
9	X-RAY DIFFRACTION	9	ALL	I	4 - 302
10	X-RAY DIFFRACTION	10	ALL	J	3 - 301
11	X-RAY DIFFRACTION	11	ALL	K	4 - 305
12	X-RAY DIFFRACTION	12	ALL	L	4 - 301

-
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