PDB-1s4e: Pyrococcus furiosus galactokinase in complex with galactose, ADP ...

ID or keywords:

Entry

Database: PDB / ID: 1s4e

Title

Pyrococcus furiosus galactokinase in complex with galactose, ADP and magnesium

Components

Galactokinase

Keywords

TRANSFERASE / GHMP kinase superfamily / P-loop

Function / homology

Function and homology information

galactokinase / galactokinase activity / galactose metabolic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.9 Å

Authors

Hartley, A. / Glynn, S.E. / Barynin, V. / Baker, P.J. / Sedelnikova, S.E. / Verhees, C. / de Geus, D. / van der Oost, J. / Timson, D.J. / Reece, R.J. / Rice, D.W.

Citation

Journal: J.Mol.Biol. / Year: 2004
Title: Substrate specificity and mechanism from the structure of Pyrococcus furiosus galactokinase
Authors: Hartley, A. / Glynn, S.E. / Barynin, V. / Baker, P.J. / Sedelnikova, S.E. / Verhees, C. / de Geus, D. / van der Oost, J. / Timson, D.J. / Reece, R.J. / Rice, D.W.

History

Deposition	Jan 16, 2004	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 6, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Apr 3, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Similar structure data	2dei-d 5z4m-d 2dej-d 2qr8-d 4yif-1 6yqq-d 1tvu-d 3s2w-2 2cz9-d 4m2m-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Galactokinase

B: Galactokinase

C: Galactokinase

D: Galactokinase

E: Galactokinase

F: Galactokinase

G: Galactokinase

H: Galactokinase

I: Galactokinase

hetero molecules

362 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Galactokinase

hetero molecules

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

2

B: Galactokinase

hetero molecules

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

3

C: Galactokinase

hetero molecules

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

4

D: Galactokinase

hetero molecules

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

5

E: Galactokinase

hetero molecules

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

6

F: Galactokinase

hetero molecules

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

7

G: Galactokinase

hetero molecules

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

8

H: Galactokinase

hetero molecules

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

9

I: Galactokinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	211.974, 355.672, 165.613
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein

Galactokinase / Galactose kinase

Mass: 39614.938 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus furiosus (archaea) / Gene: GALK / Plasmid: pET9d / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HHB6, galactokinase

#2: Sugar

ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#3: Chemical

ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg

#4: Chemical

ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE

Mass: 427.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.91 Å³/Da / Density % sol: 74.75 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulphate, Tris-HCl, galactose, ADP, magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.97950, 0.97973, 0.93928

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2001 / Details: Mirrors

Radiation

Monochromator: Double crystal Si(111) or Si(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.97973	1
3	0.93928	1

Reflection

Resolution: 2.9→25 Å / Num. obs: 137024 / % possible obs: 99.5 % / Redundancy: 3.54 % / B_iso Wilson estimate: 70 Å² / R_sym value: 0.06 / Net I/σ(I): 17.81

Reflection shell

Resolution: 2.9→2.97 Å / Mean I/σ(I) obs: 3.4 / R_sym value: 0.38

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
SCALEPACK		data scaling
MLPHARE		phasing

Refinement

Method to determine structure:

MAD
Starting model: MAD phased model

Resolution: 2.9→10 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.875 / SU B: 11.545 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26972	6821	5.1 %	RANDOM
R_work	0.23018	-	-	-
all	0.23215	134320	-	-
obs	0.23215	127499	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.44 Å²	0 Å²	0 Å²
2-	-	0.08 Å²	0 Å²
3-	-	-	2.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22351	0	360	0	22711

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	23162
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	21032
X-RAY DIFFRACTION	r_angle_refined_deg	1.659	1.982	31440
X-RAY DIFFRACTION	r_angle_other_deg	1.015	3	48409
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.063	5	2936
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	3656
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	25626
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4675
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	4918
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	23794
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.093	0.2	13969
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	374
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.262	0.2	31
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.239	0.2	101
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.115	0.2	9
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.393	1.5	14687
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.745	2	23337
X-RAY DIFFRACTION	r_scbond_it	1.708	3	8475
X-RAY DIFFRACTION	r_scangle_it	2.376	4.5	8103
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.969 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.308	483
R_work	0.248	8772

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	7.8911	3.0287	0.2647	3.771	0.744	2.5938	-0.6332	1.5124	-0.0106	-0.5652	0.7235	0.7685	0.2387	-0.51	-0.0903	0.5008	-0.3823	-0.0878	0.7907	0.1953	0.6768	61.972	58.478	56.709
2	3.4896	-0.2334	0.0904	3.9907	-0.7925	1.612	-0.035	0.1332	0.0122	0.1774	0.0862	0.2537	-0.0684	0.0507	-0.0512	0.2242	-0.1259	0.053	0.2074	0.073	0.2928	83.049	63.216	67.599
3	5.4511	1.3283	0.1249	6.1657	-0.7488	3.3914	-0.9475	2.1017	0.9063	-1.1766	0.8265	-0.1774	-0.6555	0.2473	0.1211	1.1558	-0.5039	0.0756	1.176	0.3798	0.577	24.949	61.474	60.591
4	4.6656	0.0143	-0.6414	3.5554	1.331	4.5944	-0.3396	1.0977	-0.2778	-0.8235	0.2325	0.071	-0.0052	-0.1904	0.1071	0.476	-0.1739	0.1248	0.4432	0.034	0.2136	10.314	47.804	72.329
5	3.7535	-0.0548	-0.6518	3.9455	-1.5057	3.9498	-0.1854	-0.4559	-1.2813	0.5751	-0.046	0.139	0.4878	0.2244	0.2314	0.6322	0.0375	0.0668	0.4089	0.1893	1.1004	93.516	23.465	79.846
6	4.9926	0.991	-0.8022	3.7078	-0.4953	3.0006	-0.17	0.7629	-1.0229	-0.274	-0.0987	-0.0266	0.6626	0.3863	0.2687	0.4311	0.0576	-0.0379	0.5792	-0.2714	0.7833	103.8	27.74	58.179
7	5.125	1.2004	1.3249	3.5599	1.1374	3.9776	-0.2086	0.1042	0.7799	-0.146	-0.1194	-0.1341	-0.6109	-0.0803	0.328	0.4876	0.1332	-0.2973	0.2991	0.1245	0.7187	166.929	142.753	83.668
8	4.6624	0.5166	0.4654	2.2789	-1.1994	2.6509	-0.0696	0.8218	-0.4243	-0.3478	0.0501	0.0395	0.068	-0.0314	0.0195	0.4299	0.1102	-0.2636	0.4781	-0.0522	0.5151	152.691	125.615	71.86
9	6.8083	-0.3511	2.3425	1.8296	-0.4972	4.8334	-0.3908	0.6812	0.2975	0.1423	0.0245	0.006	-0.4012	0.2466	0.3663	0.3625	0.0462	-0.1434	0.5475	0.1638	0.3758	154.012	47.374	78.515
10	5.5733	-1.1694	0.3179	2.234	-0.5293	2.165	-0.0528	0.8041	-0.4242	-0.061	-0.1648	0.2219	0.0908	0.2615	0.2176	0.3234	-0.0798	-0.1898	0.7892	0.0891	0.4754	130.549	41.844	69.887
11	1.9817	0.5199	0.0183	1.9964	-0.2803	3.8445	0.0511	-0.0623	-0.1474	-0.0245	0.0257	-0.2958	-0.2784	0.3975	-0.0768	0.3082	-0.0411	0.0456	0.1371	0.0217	0.2791	117.967	109.744	54.893
12	2.2995	-0.1697	0.524	2.4414	1.138	1.6881	-0.0648	-0.1889	-0.2321	0.2077	0.0177	0.0879	-0.0168	-0.2142	0.0471	0.2599	-0.0626	0.083	0.1581	0.1573	0.246	95.652	103.853	66.607
13	4.9283	4.9272	1.1128	10.8006	0.9186	10.1046	-1.1526	1.2597	1.4601	-2.6634	-0.0621	1.6877	-0.3694	-0.2228	1.2147	1.5278	-0.0892	-0.3634	1.0195	-0.0109	0.9322	2.944	121.25	66.931
14	5.596	0.754	-1.7647	4.4371	0.3648	5.8432	-0.4747	0.5466	-1.1318	-1.3907	0.2107	-0.4759	0.7895	0.1503	0.264	0.8451	0.1212	0.2093	0.4122	-0.128	0.6655	1.375	105.478	79.432
15	3.6243	-0.2641	0.0942	2.6852	0.5241	3.6311	-0.0396	0.0366	0.3838	-0.1928	-0.1164	0.617	-0.5076	-0.8868	0.1561	0.2753	0.1336	-0.0937	0.4941	-0.0788	0.4361	64.516	148.21	46.791
16	3.632	0.3017	-1.0711	1.1873	-0.16	2.1546	-0.0725	-0.1973	-0.192	0.1028	0.0422	0.3001	0.2916	-0.3133	0.0304	0.1998	-0.0295	0.0143	0.1737	0.0288	0.1946	79.192	131.076	57.94
17	2.5916	0.2565	-0.7395	1.7464	0.9875	3.3934	-0.0886	-0.0095	0.1556	-0.0206	0.1104	-0.2451	-0.1333	0.2569	-0.0218	0.2117	-0.015	-0.0661	0.1058	-0.0387	0.0776	118.042	150.173	56.217
18	1.767	1.0651	0.2129	2.831	-0.0009	2.4481	-0.0135	-0.3469	0.1337	0.1461	0.0571	0.1283	-0.2834	-0.0707	-0.0437	0.2972	0.0908	-0.0209	0.1752	-0.1181	0.101	105.995	157.002	77.645

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	5 - 12	5 - 12
2	X-RAY DIFFRACTION	1	A	A	29 - 161	29 - 161
3	X-RAY DIFFRACTION	1	A	A	346 - 351	346 - 351
4	X-RAY DIFFRACTION	2	A	A	13 - 28	13 - 28
5	X-RAY DIFFRACTION	2	A	A	162 - 345	162 - 345
6	X-RAY DIFFRACTION	3	B	B	8 - 12	8 - 12
7	X-RAY DIFFRACTION	3	B	B	29 - 161	29 - 161
8	X-RAY DIFFRACTION	3	B	B	346 - 349	346 - 349
9	X-RAY DIFFRACTION	4	B	B	13 - 28	13 - 28
10	X-RAY DIFFRACTION	4	B	B	162 - 345	162 - 345
11	X-RAY DIFFRACTION	5	C	C	4 - 12	4 - 12
12	X-RAY DIFFRACTION	5	C	C	29 - 161	29 - 161
13	X-RAY DIFFRACTION	5	C	C	346 - 350	346 - 350
14	X-RAY DIFFRACTION	6	C	C	13 - 28	13 - 28
15	X-RAY DIFFRACTION	6	C	C	162 - 345	162 - 345
16	X-RAY DIFFRACTION	7	D	D	2 - 12	2 - 12
17	X-RAY DIFFRACTION	7	D	D	29 - 161	29 - 161
18	X-RAY DIFFRACTION	7	D	D	346 - 352	346 - 352
19	X-RAY DIFFRACTION	8	D	D	13 - 28	13 - 28
20	X-RAY DIFFRACTION	8	D	D	162 - 345	162 - 345
21	X-RAY DIFFRACTION	9	E	E	3 - 12	3 - 12
22	X-RAY DIFFRACTION	9	E	E	29 - 161	29 - 161
23	X-RAY DIFFRACTION	9	E	E	346 - 352	346 - 352
24	X-RAY DIFFRACTION	10	E	E	13 - 28	13 - 28
25	X-RAY DIFFRACTION	10	E	E	162 - 345	162 - 345
26	X-RAY DIFFRACTION	11	F	F	2 - 12	2 - 12
27	X-RAY DIFFRACTION	11	F	F	29 - 161	29 - 161
28	X-RAY DIFFRACTION	11	F	F	346 - 352	346 - 352
29	X-RAY DIFFRACTION	12	F	F	13 - 28	13 - 28
30	X-RAY DIFFRACTION	12	F	F	162 - 345	162 - 345
31	X-RAY DIFFRACTION	13	G	G	11 - 12	11 - 12
32	X-RAY DIFFRACTION	13	G	G	29 - 158	29 - 158
33	X-RAY DIFFRACTION	13	G	G	346 - 347	346 - 347
34	X-RAY DIFFRACTION	14	G	G	13 - 28	13 - 28
35	X-RAY DIFFRACTION	14	G	G	162 - 345	162 - 345
36	X-RAY DIFFRACTION	15	H	H	2 - 12	2 - 12
37	X-RAY DIFFRACTION	15	H	H	29 - 161	29 - 161
38	X-RAY DIFFRACTION	15	H	H	346 - 350	346 - 350
39	X-RAY DIFFRACTION	16	H	H	13 - 28	13 - 28
40	X-RAY DIFFRACTION	16	H	H	162 - 345	162 - 345
41	X-RAY DIFFRACTION	17	I	I	2 - 12	2 - 12
42	X-RAY DIFFRACTION	17	I	I	29 - 161	29 - 161
43	X-RAY DIFFRACTION	17	I	I	346 - 352	346 - 352
44	X-RAY DIFFRACTION	18	I	I	13 - 28	13 - 28
45	X-RAY DIFFRACTION	18	I	I	162 - 345	162 - 345

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