PDB-2be4: X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO Dr.36843

ID or keywords:

Entry

Database: PDB / ID: 2be4

Title

X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO Dr.36843

Components

hypothetical protein LOC449832

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Dr.36843 / BC083168 / CALICIUM BINDING / EF-HAND SUPERFAMILY / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG

Function / homology

Function and homology information

spinal cord motor neuron differentiation / terminal bouton / brain development / synapse / dendrite / calcium ion binding / nucleus / cytosol
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Wesenberg, G.E. / Phillips Jr., G.N. / Han, B.W. / Bitto, E. / Bingman, C.A. / Bae, E. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Proteins / Year: 2009
Title: X-ray structure of Danio rerio secretagogin: A hexa-EF-hand calcium sensor.
Authors: Bitto, E. / Bingman, C.A. / Bittova, L. / Frederick, R.O. / Fox, B.G. / Phillips Jr., G.N.

History

Deposition	Oct 21, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 1, 2005	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	Feb 6, 2013	Group: Database references
Revision 1.4	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2be4.cif.gz	78.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2be4.ent.gz	55.8 KB	Display	PDB format
PDBx/mmJSON format	2be4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/be/2be4 ftp://data.pdbj.org/pub/pdb/validation_reports/be/2be4	HTTPS FTP

-
Related structure data

Similar structure data	6pqb-3 2q4u-d 5cb1-2 3qij-1 4reg-d 3tz0-d 4dzy-d 7dc4-d 5bw0-1 2o70-3 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	TargetDB: GO.74073

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: hypothetical protein LOC449832

32.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	47.884, 52.748, 114.364
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	hypothetical protein LOC449832 Mass: 32050.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: Dr.36843, BC083168 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q5XJX1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.9 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 10 MG/ML PROTEIN, 26% PEG 2K, 0.100 M BTP, pH 9.0, vapor diffusion, hanging drop, temperature 277K

-
Data collection

Diffraction

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

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97911, 0.96411

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

Monochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97911	1
2	0.96411	1

Reflection

D res low: 80 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	D res high (Å)	% possible obs
8.4	1	17378	0.093	1.33	2.1	98.8
7.7	2	16159	0.076	0.989	2.15	98.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.18	80	99.1	1	0.075	1.591	7.7
4.11	5.18	99.6	1	0.065	1.252	8.4
3.59	4.11	99.4	1	0.072	1.357	8.5
3.26	3.59	99.1	1	0.08	1.446	8.6
3.03	3.26	99.2	1	0.095	1.811	8.6
2.85	3.03	99.1	1	0.111	1.612	8.6
2.71	2.85	99	1	0.132	1.562	8.6
2.59	2.71	98.6	1	0.164	1.421	8.7
2.49	2.59	98.5	1	0.208	1.311	8.8
2.4	2.49	99.6	1	0.233	1.241	8.7
2.33	2.4	98	1	0.266	1.17	8.7
2.26	2.33	97.7	1	0.31	1.101	8.6
2.2	2.26	99.7	1	0.369	1.011	8.3
2.15	2.2	96.6	1	0.435	0.959	7.9
2.1	2.15	98.3	1	0.51	0.92	6.9
5.3	80	99.3	2	0.05	0.981	7.3
4.21	5.3	99.5	2	0.05	0.96	7.8
3.68	4.21	99.5	2	0.056	1.032	7.9
3.34	3.68	99.6	2	0.066	1.049	8.1
3.1	3.34	99.3	2	0.083	1.063	8.1
2.92	3.1	98.8	2	0.103	1.067	8.2
2.77	2.92	99.4	2	0.13	1.088	8.2
2.65	2.77	99.3	2	0.171	1.103	8.2
2.55	2.65	98.7	2	0.223	1.051	8.2
2.46	2.55	98.4	2	0.262	0.934	8.2
2.38	2.46	98.8	2	0.297	0.93	8.1
2.32	2.38	99	2	0.338	0.936	7.7
2.26	2.32	95.9	2	0.399	0.839	7.3
2.2	2.26	96.9	2	0.462	0.837	6.5
2.15	2.2	89.6	2	0.539	0.824	5.6

Reflection

Resolution: 2.1→80 Å / Num. obs: 17378 / % possible obs: 98.8 % / Redundancy: 8.4 % / R_merge(I) obs: 0.093 / Χ²: 1.33 / Net I/σ(I): 11.052

Reflection shell

Resolution: 2.1→2.15 Å / % possible obs: 98.3 % / Redundancy: 6.9 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 2.779 / Num. measured obs: 1103 / Χ²: 0.92 / % possible all: 98.3

-
Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 2.1 Å / Lowest resolution: 38.77 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	14970	2245
ISO_2	0.793	0.827	1.377	1.177	13861	2128
ANO_1	0.626	0	1.568	0	14923	0
ANO_2	0.765	0	1.137	0	13672	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	9.14-38.77	0	0	0	0	136	111
ISO_1	6.56-9.14	0	0	0	0	276	115
ISO_1	5.38-6.56	0	0	0	0	378	121
ISO_1	4.67-5.38	0	0	0	0	450	119
ISO_1	4.18-4.67	0	0	0	0	523	114
ISO_1	3.82-4.18	0	0	0	0	583	114
ISO_1	3.54-3.82	0	0	0	0	630	119
ISO_1	3.31-3.54	0	0	0	0	693	112
ISO_1	3.13-3.31	0	0	0	0	734	108
ISO_1	2.97-3.13	0	0	0	0	778	104
ISO_1	2.83-2.97	0	0	0	0	819	91
ISO_1	2.71-2.83	0	0	0	0	864	119
ISO_1	2.6-2.71	0	0	0	0	903	115
ISO_1	2.51-2.6	0	0	0	0	930	115
ISO_1	2.42-2.51	0	0	0	0	977	113
ISO_1	2.35-2.42	0	0	0	0	1004	117
ISO_1	2.28-2.35	0	0	0	0	1012	111
ISO_1	2.21-2.28	0	0	0	0	1078	110
ISO_1	2.15-2.21	0	0	0	0	1088	115
ISO_1	2.1-2.15	0	0	0	0	1114	102
ANO_1	9.14-38.77	0.482	0	2.073	0	136	0
ANO_1	6.56-9.14	0.426	0	2.479	0	276	0
ANO_1	5.38-6.56	0.412	0	2.599	0	378	0
ANO_1	4.67-5.38	0.471	0	2.396	0	450	0
ANO_1	4.18-4.67	0.522	0	2.135	0	523	0
ANO_1	3.82-4.18	0.488	0	2.253	0	583	0
ANO_1	3.54-3.82	0.515	0	2.225	0	630	0
ANO_1	3.31-3.54	0.517	0	2.193	0	693	0
ANO_1	3.13-3.31	0.514	0	2.081	0	733	0
ANO_1	2.97-3.13	0.54	0	1.895	0	777	0
ANO_1	2.83-2.97	0.597	0	1.602	0	817	0
ANO_1	2.71-2.83	0.673	0	1.371	0	862	0
ANO_1	2.6-2.71	0.72	0	1.228	0	898	0
ANO_1	2.51-2.6	0.779	0	1.059	0	927	0
ANO_1	2.42-2.51	0.834	0	0.888	0	971	0
ANO_1	2.35-2.42	0.872	0	0.788	0	999	0
ANO_1	2.28-2.35	0.912	0	0.673	0	1012	0
ANO_1	2.21-2.28	0.955	0	0.603	0	1070	0
ANO_1	2.15-2.21	0.966	0	0.496	0	1084	0
ANO_1	2.1-2.15	0.983	0	0.458	0	1104	0
ISO_2	9.14-38.77	0.604	0.713	2.586	1.793	136	111
ISO_2	6.56-9.14	0.574	0.755	2.653	1.569	276	115
ISO_2	5.38-6.56	0.651	0.882	2.396	1.534	378	121
ISO_2	4.67-5.38	0.697	0.74	1.794	1.255	450	119
ISO_2	4.18-4.67	0.765	0.817	1.447	1.126	523	114
ISO_2	3.82-4.18	0.767	0.776	1.313	0.94	583	114
ISO_2	3.54-3.82	0.837	0.938	1.24	0.943	630	119
ISO_2	3.31-3.54	0.824	0.863	1.194	1.017	693	112
ISO_2	3.13-3.31	0.847	0.83	1.247	0.893	734	108
ISO_2	2.97-3.13	0.863	0.938	1.297	0.786	778	104
ISO_2	2.83-2.97	0.833	0.859	1.193	0.953	819	91
ISO_2	2.71-2.83	0.828	0.881	1.125	0.701	864	119
ISO_2	2.6-2.71	0.847	0.992	1.108	0.752	903	115
ISO_2	2.51-2.6	0.858	1.015	0.991	0.555	930	115
ISO_2	2.42-2.51	0.861	0.991	0.919	0.51	977	113
ISO_2	2.35-2.42	0.878	0.93	0.759	0.424	1003	117
ISO_2	2.28-2.35	0.914	0.937	0.639	0.482	1006	109
ISO_2	2.21-2.28	0.918	1.045	0.523	0.334	1049	104
ISO_2	2.15-2.21	0.948	0.971	0.452	0.358	1033	99
ISO_2	2.1-2.15	0.962	1.365	0.48	0.354	96	9
ANO_2	9.14-38.77	0.491	0	2.089	0	136	0
ANO_2	6.56-9.14	0.433	0	2.657	0	276	0
ANO_2	5.38-6.56	0.42	0	2.79	0	378	0
ANO_2	4.67-5.38	0.504	0	2.407	0	450	0
ANO_2	4.18-4.67	0.573	0	2.083	0	523	0
ANO_2	3.82-4.18	0.551	0	1.985	0	582	0
ANO_2	3.54-3.82	0.611	0	1.908	0	630	0
ANO_2	3.31-3.54	0.648	0	1.659	0	693	0
ANO_2	3.13-3.31	0.676	0	1.542	0	733	0
ANO_2	2.97-3.13	0.718	0	1.257	0	777	0
ANO_2	2.83-2.97	0.808	0	1.002	0	818	0
ANO_2	2.71-2.83	0.872	0	0.799	0	862	0
ANO_2	2.6-2.71	0.896	0	0.62	0	901	0
ANO_2	2.51-2.6	0.921	0	0.546	0	929	0
ANO_2	2.42-2.51	0.958	0	0.475	0	974	0
ANO_2	2.35-2.42	0.963	0	0.389	0	995	0
ANO_2	2.28-2.35	0.982	0	0.353	0	983	0
ANO_2	2.21-2.28	0.988	0	0.3	0	1001	0
ANO_2	2.15-2.21	0.994	0	0.242	0	942	0
ANO_2	2.1-2.15	0.999	0	0.28	0	89	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-7.282	-49.407	-29.891	SE	34.61	2.05
2	-2.426	-39.613	-105.482	SE	38.21	1.64
3	-2.724	-37.796	-75.983	SE	63.06	1.67
4	-3.015	-40.084	-28.856	SE	46.38	1.32
5	-0.923	-48.105	-64.034	SE	38.5	1.6
6	-1.444	-41.105	-32.678	SE	43.72	1.3
7	-4.784	-9.296	-65.867	SE	39.33	1.61
8	-4.271	-11.135	-94.391	SE	44.99	1.3

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 17330

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.16-100	68.1	0.83	502
5.63-7.16	57.4	0.899	506
4.88-5.63	51.2	0.924	506
4.41-4.88	51.2	0.912	505
4.08-4.41	49.4	0.914	511
3.83-4.08	54.1	0.926	506
3.63-3.83	56.6	0.904	505
3.46-3.63	56	0.908	530
3.31-3.46	56.6	0.888	553
3.18-3.31	55	0.891	579
3.06-3.18	56.7	0.885	602
2.96-3.06	54.8	0.897	614
2.86-2.96	58.7	0.88	637
2.78-2.86	60.5	0.881	667
2.7-2.78	56.6	0.869	671
2.62-2.7	59.3	0.858	687
2.56-2.62	63.2	0.866	715
2.49-2.56	64.1	0.86	723
2.44-2.49	66	0.863	741
2.38-2.44	70	0.89	753
2.33-2.38	68.4	0.868	779
2.28-2.33	70.5	0.871	773
2.24-2.28	76.9	0.882	822
2.2-2.24	78.7	0.838	817
2.16-2.2	79.4	0.856	826
2.1-2.16	79.9	0.776	1300

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
PHENIX		phasing
SHELXD		phasing
SOLOMON		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.1→57.166 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.931 / WR_factor R_free: 0.258 / WR_factor R_work: 0.181 / SU B: 10.21 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.209
Details: SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.00, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2529	885	5.105 %	RANDOM
R_work	0.1755	-	-	-
all	0.179	-	-	-
obs	0.17937	17336	98.826 %	-

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: 41.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.965 Å²	0 Å²	0 Å²
2-	-	-0.854 Å²	0 Å²
3-	-	-	-0.111 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→57.166 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2203	0	0	240	2443

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	2247
X-RAY DIFFRACTION	r_angle_refined_deg	1.586	1.972	3011
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.731	5	269
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.854	24.957	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.312	15	439
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.609	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	317
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1698
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1072
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	1557
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.206	0.2	176
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.191	0.2	40
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.146	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	1.687	2	1397
X-RAY DIFFRACTION	r_mcangle_it	2.87	4	2155
X-RAY DIFFRACTION	r_scbond_it	4.811	6	962
X-RAY DIFFRACTION	r_scangle_it	6.373	8	856

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.154	0.37	68	0.207	1144	1233	98.297
2.154-2.213	0.266	59	0.2	1150	1247	96.953
2.213-2.277	0.266	59	0.188	1145	1218	98.851
2.277-2.347	0.285	58	0.185	1078	1151	98.697
2.347-2.424	0.239	66	0.19	1065	1154	98.007
2.424-2.509	0.296	53	0.187	1039	1110	98.378
2.509-2.603	0.23	52	0.202	999	1053	99.81
2.603-2.709	0.344	54	0.189	964	1034	98.453
2.709-2.829	0.282	57	0.177	932	1000	98.9
2.829-2.967	0.29	47	0.184	890	947	98.944
2.967-3.127	0.259	54	0.172	842	905	99.006
3.127-3.316	0.233	43	0.17	808	858	99.184
3.316-3.544	0.352	34	0.159	782	819	99.634
3.544-3.827	0.231	43	0.153	705	752	99.468
3.827-4.191	0.164	39	0.149	665	706	99.717
4.191-4.682	0.163	24	0.154	613	640	99.531
4.682-5.4	0.246	22	0.17	556	581	99.484
5.4-6.599	0.319	22	0.221	468	491	99.796
6.599-9.271	0.276	25	0.206	367	393	99.746
9.271-57.166	0.122	6	0.165	239	250	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	2.814	-0.0976	-2.4164	2.1463	-0.5801	7.563	0.132	0.1802	0.1707	-0.0549	0.004	0.2961	-0.0335	-0.3826	-0.1361	-0.1362	0.0267	-0.0173	-0.1652	-0.0016	-0.0937	-21.336	-4.57	28.62
2	5.8022	1.0514	0.2587	2.9654	0.5404	3.8697	0.0498	0.1014	-0.1004	-0.0855	-0.083	-0.0782	0.1012	0.0156	0.0333	-0.1164	0.0078	0.0196	-0.1819	0.0232	-0.2027	-4.288	-5.596	49.812
3	8.7373	2.906	-1.9578	8.2647	-0.8259	4.5808	-0.2059	0.3414	-0.2703	0.0509	0.1182	0.6224	0.2117	-0.7777	0.0877	-0.0941	-0.0483	0.0267	0.0149	-0.004	-0.0863	3.279	15.748	42.792

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	3 - 85	3 - 85
2	2	86 - 181	86 - 181
3	3	185 - 272	185 - 272

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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