PDB-4gmd: The crystal structure of thymidylate kinase from Pseudomonas aeru...

ID or keywords:

Entry

Database: PDB / ID: 4gmd

Title

The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with AZT Monophosphate

Components

Thymidylate kinase

Keywords

Transferase/Inhibitor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / PROTEIN STRUCTURE INITIATIVE / TRANSFERASE / Transferase-Inhibitor complex

Function / homology

Function and homology information

dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Citation

Journal: To be Published
Title: The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with AZT Monophosphate
Authors: Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A.

History

Deposition	Aug 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4gmd.cif.gz	330.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4gmd.ent.gz	270.5 KB	Display	PDB format
PDBx/mmJSON format	4gmd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4gmd_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	4gmd_full_validation.pdf.gz	1.6 MB	Display
Data in XML	4gmd_validation.xml.gz	35.1 KB	Display
Data in CIF	4gmd_validation.cif.gz	47.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gm/4gmd ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gmd	HTTPS FTP

-
Related structure data

Related structure data	4e5uS 4edh 4esh S: Starting model for refinement
Similar structure data	4edh-d 3uwk-3 3uxm-6 2qkk-5 5xt8-d 2nrh-d 2zi4-1 2jas-3 4esh-2 5x8v-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: APC105732

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thymidylate kinase

B: Thymidylate kinase

C: Thymidylate kinase

D: Thymidylate kinase

hetero molecules

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

1

A: Thymidylate kinase

C: Thymidylate kinase

hetero molecules

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

2

B: Thymidylate kinase

D: Thymidylate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	44.500, 123.404, 73.920
Angle α, β, γ (deg.)	90.00, 100.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Experimentally unknown. The chains A and B, C and D may form dimers, respectively.

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Thymidylate kinase / dTMP kinase Mass: 23408.600 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2962, tmk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HZN8, dTMP kinase

#1: Protein

Thymidylate kinase / dTMP kinase

Mass: 23408.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2962, tmk / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HZN8, dTMP kinase

-
Non-polymers , 5 types, 326 molecules

#2: Chemical	ChemComp-ATM / 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.13 Å³/Da / Density % sol: 42.38 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M CaCl2, 0.1M Tris:HCl, 20%(w/v) PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2012 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 1.98→34 Å / Num. all: 54559 / Num. obs: 54559 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.069 / Net I/σ(I): 24.4
Reflection shell	Resolution: 1.98→2.01 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.611 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2763 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4E5U

4e5u

Resolution: 1.98→34 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 24.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2257	2767	5.08 %	random
R_work	0.1772	-	-	-
all	0.1797	54514	-	-
obs	0.1797	54514	99.81 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 35.786 Å² / k_sol: 0.302 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.7397 Å²	-0 Å²	3.4182 Å²
2-	-	-8.035 Å²	-0 Å²
3-	-	-	0.2953 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6172	0	117	312	6601

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6379
X-RAY DIFFRACTION	f_angle_d	1.002	8643
X-RAY DIFFRACTION	f_dihedral_angle_d	14.036	2428
X-RAY DIFFRACTION	f_chiral_restr	0.065	965
X-RAY DIFFRACTION	f_plane_restr	0.005	1155

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 (%)
1.9798-2.0139	0.2925	131	0.2336	2596	X-RAY DIFFRACTION	98
2.0139-2.0505	0.2912	142	0.2152	2561	X-RAY DIFFRACTION	100
2.0505-2.09	0.2354	138	0.2212	2563	X-RAY DIFFRACTION	100
2.09-2.1326	0.3073	118	0.2079	2594	X-RAY DIFFRACTION	100
2.1326-2.179	0.2852	134	0.2063	2597	X-RAY DIFFRACTION	100
2.179-2.2297	0.2758	149	0.1999	2582	X-RAY DIFFRACTION	100
2.2297-2.2854	0.2337	136	0.1883	2567	X-RAY DIFFRACTION	100
2.2854-2.3472	0.2706	134	0.1901	2617	X-RAY DIFFRACTION	100
2.3472-2.4162	0.2875	154	0.1977	2541	X-RAY DIFFRACTION	100
2.4162-2.4942	0.2686	129	0.1996	2612	X-RAY DIFFRACTION	100
2.4942-2.5833	0.2669	136	0.1964	2579	X-RAY DIFFRACTION	100
2.5833-2.6867	0.249	142	0.2087	2547	X-RAY DIFFRACTION	100
2.6867-2.8089	0.2621	143	0.2052	2629	X-RAY DIFFRACTION	100
2.8089-2.957	0.2618	132	0.2071	2606	X-RAY DIFFRACTION	100
2.957-3.1421	0.2669	135	0.1937	2576	X-RAY DIFFRACTION	100
3.1421-3.3845	0.2346	145	0.1837	2587	X-RAY DIFFRACTION	100
3.3845-3.7247	0.2181	148	0.167	2594	X-RAY DIFFRACTION	100
3.7247-4.2628	0.194	140	0.1465	2570	X-RAY DIFFRACTION	100
4.2628-5.3673	0.1437	149	0.1355	2605	X-RAY DIFFRACTION	100
5.3673-34.0418	0.2143	132	0.1696	2624	X-RAY DIFFRACTION	99

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	2.1222	-0.3587	1.3868	5.184	0.5789	1.9624	-0.0991	-0.4428	-0.0865	0.0667	0.2406	0.2332	0.0216	-0.248	-0.1005	0.5039	0.0492	0.0122	0.3891	0.0305	0.3349	15.4043	-54.3839	15.518
2	0.5698	0.1276	0.2692	2.8315	0.3957	1.5364	0.0143	0.0245	-0.0489	-0.3743	-0.0381	0.0428	0.0464	0.0275	0.0202	0.2809	0.0271	0.0019	0.2589	0.013	0.2741	18.3806	-39.5276	23.2638
3	1.7416	-0.9352	0.631	0.5307	-0.8187	6.9073	0.4004	-0.7654	-0.7635	0.1806	-0.101	0.519	0.3933	-1.1774	-0.181	0.5022	-0.0587	-0.0038	0.6377	0.1331	0.8444	1.2117	-43.6498	30.5451
4	4.4791	-0.3783	-1.3729	3.9768	1.3469	7.0718	0.5776	0.4149	0.1869	-0.6647	-0.2327	0.9845	-0.5165	-0.9463	0.0513	0.5182	0.1885	-0.2656	0.3771	-0.005	0.4322	2.9236	-37.0251	16.8532
5	1.3835	-1.2122	0.6164	5.1236	0.4468	2.4649	0.4258	0.2927	-0.0009	-1.7739	-0.272	0.5078	-0.2713	0.2333	0.0211	0.8934	0.1289	-0.0841	0.4159	0.0185	0.442	10.9372	-51.896	7.2641
6	6.9183	1.0793	1.3644	3.5001	1.0273	3.8871	-0.393	0.708	0.029	0.2132	0.4324	-0.2511	-0.1074	0.3893	-0.0087	0.3248	0.0452	-0.0059	0.3788	0.018	0.3481	33.1612	-29.5194	-5.3736
7	5.0456	3.5006	1.6759	6.0441	1.9801	2.1055	-0.1081	0.1159	-0.5416	-0.2548	0.1917	-0.8534	-0.2546	0.2569	-0.001	0.4825	0.0471	0.0467	0.3295	0.0156	0.3981	32.4863	-33.6658	-16.2996
8	0.7707	0.2687	0.2835	2.7345	1.8205	3.036	-0.0035	0.1871	-0.0281	-0.6867	0.0584	-0.4809	-0.3452	0.2789	-0.0077	0.4025	0.1004	0.0793	0.3624	0.0377	0.3557	29.5431	-14.7693	-4.2889
9	0.8173	0.1558	-0.1685	1.6117	0.5577	0.7095	0.0802	0.1477	-0.1561	-0.1356	-0.0649	-0.047	0.023	0.0042	-0.0223	0.3121	0.0715	0.0198	0.351	0.0119	0.2772	28.4692	-22.13	1.6518
10	1.4114	-0.2362	0.518	2.025	0.8573	2.3651	0.0771	0.0813	-0.1079	0.3221	0.0146	0.0082	0.4306	-0.0034	-0.0972	0.3964	0.0493	0.0262	0.312	0.0188	0.3528	29.0411	-28.1575	6.1517
11	0.9541	-0.558	-0.7444	0.9878	-0.4573	1.6934	0.0236	0.9393	1.2489	0.05	-0.0174	-0.3757	-0.4528	-0.0007	-0.1838	0.3126	-0.115	0.1467	0.7265	-0.0596	0.927	45.8837	-16.6664	-0.6161
12	4.0651	2.6415	-0.1357	6.2828	0.5766	2.1676	0.3904	-0.3733	0.2465	0.5633	-0.3833	-0.5314	0.1954	0.7863	0.0379	0.3245	0.1133	-0.0257	0.5299	0.0076	0.4845	44.1124	-26.9152	5.8513
13	5.1385	0.423	-2.5976	3.7581	-0.1402	6.5753	0.2006	0.0415	-0.607	0.2752	0.0976	-0.2215	0.3002	-0.1375	-0.3945	0.3911	0.0764	-0.0073	0.4556	-0.0052	0.4663	39.6947	-36.9787	-1.7781
14	7.7775	0.2404	2.0492	4.3404	0.728	6.4304	0.1474	-0.0596	-0.3503	1.1391	0.6124	-0.241	1.3146	0.6735	-0.7694	0.7768	0.1677	-0.1405	0.3963	-0.0779	0.5789	34.8865	-41.3401	-10.4955
15	5.6847	-0.2138	1.1138	1.9851	0.3293	3.5847	-0.0484	-0.4304	-0.3703	0.1776	0.1393	-0.1609	-0.1953	-0.2407	0.0243	0.462	-0.0804	-0.0591	0.2982	0.0059	0.2465	28.1263	-14.8012	44.5601
16	4.1667	-3.6551	-1.0343	5.4038	1.4835	1.0507	-0.5521	-0.4163	-0.2362	1.1977	0.3708	0.095	0.0903	0.1533	0.1975	0.5621	0.0036	-0.018	0.4384	-0.0024	0.3601	25.0699	-10.1121	54.6819
17	1.0434	-0.6664	0.0159	2.3586	0.3564	1.5629	-0.1166	-0.0532	-0.0082	0.2274	0.0314	-0.0725	0.0058	-0.0154	0.0874	0.2142	-0.0065	-0.0259	0.2897	0.0161	0.2782	21.8299	-25.5576	40.1985
18	1.4208	0.1825	-0.5669	1.8664	0.0663	2.7305	0.0445	-0.0058	0.1499	-0.2358	-0.1467	-0.2176	-0.3768	0.3761	0.0907	0.3216	0.005	-0.0254	0.3135	0.0395	0.3287	29.3471	-19.0817	32.8723
19	3.512	-0.0111	0.9881	1.0853	1.4479	2.2164	0.3493	-0.7356	-0.2789	0.6872	-0.1035	-0.7652	0.0236	0.5805	0.2086	0.4493	-0.0507	-0.1481	0.7595	0.0411	0.7346	39.4264	-31.1377	43.5317
20	2.9229	-1.7313	0.6614	4.0008	0.4527	1.5931	0.0944	0.1322	0.1952	0.0933	-0.2763	-0.894	-0.1532	1.3184	0.0596	0.3036	-0.1173	-0.0701	0.7238	0.0786	0.5124	41.3413	-18.7236	36.5274
21	3.2446	-0.4609	3.1958	1.5481	0.0622	6.8706	-0.2869	0.0764	0.509	-0.371	0.0185	-0.2075	-0.6276	0.431	0.2063	0.5176	-0.1226	-0.1013	0.5866	0.0095	0.429	36.172	-8.0603	42.5155
22	6.3701	-1.0713	1.732	2.8393	-0.8485	3.7841	-0.1019	0.2883	0.1982	-0.1317	0.2371	-0.4811	-0.6429	0.4417	-0.0145	0.5285	-0.1006	0.0502	0.4792	-0.1235	0.5522	28.466	-2.5814	49.2465
23	2.3424	0.6857	-0.0683	2.9128	0.435	1.3994	0.097	0.1992	0.2532	-0.0527	-0.1085	0.19	0.1828	-0.1567	0.0361	0.348	-0.0086	0.0298	0.3093	0.0135	0.3362	18.9967	10.7572	21.2351
24	1.0178	0.0225	-0.1228	2.3162	1.4651	1.4048	-0.0082	0.1588	0.0718	-0.353	-0.0239	-0.0227	-0.3068	0.0089	-0.0122	0.2904	0.0495	0.0368	0.3074	0.0482	0.2955	24.5135	-1.8755	10.6741
25	2.0504	-0.6464	0.0265	4.1476	-0.2216	2.2129	-0.0009	-0.0187	-0.0439	0.2902	0.011	0.203	0.1243	0.0349	0.0541	0.2743	0.0275	0.0452	0.2771	0.0279	0.2717	16.8397	-7.9751	18.1653
26	4.0229	-1.794	-1.5581	2.2177	0.6975	2.6289	0.3408	0.8141	0.7677	-0.1205	-0.6358	0.2687	-0.2932	-1.0545	0.1587	0.389	0.0885	-0.0783	0.5882	0.0072	0.5841	7.2445	-1.0272	4.5233
27	4.149	-0.0599	1.902	3.31	1.7479	9.7505	0.1225	-0.1422	0.3565	0.1305	-0.1553	1.1011	0.4944	-1.2622	-0.0667	0.2886	0.0137	0.0986	0.396	0.0043	0.5868	4.6927	-4.9286	17.0111
28	2.8116	-2.196	1.4924	4.4218	-1.3143	1.951	-0.4732	-0.4977	-0.0315	0.5823	0.2007	-0.1272	0.1083	-0.0457	0.1481	0.4035	0.1495	0.0639	0.4072	0.0131	0.3522	8.9976	3.5405	26.0519
29	4.3897	-1.3338	1.2152	3.7842	-1.0228	3.5843	-0.2572	-0.5569	-0.0288	0.3294	0.1549	0.1863	-0.254	-0.3662	0.1104	0.4357	-0.0272	0.0499	0.3279	-0.0288	0.2681	15.4516	11.6234	30.1764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:30)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 31:136)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 137:159)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 160:177)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 178:209)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 2:15)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 16:30)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 31:62)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 63:112)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 113:136)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 137:159)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 160:176)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 177:189)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 190:208)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 2:15)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 16:30)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 31:95)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 96:136)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 137:159)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 160:176)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 177:189)
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 190:209)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 2:30)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 31:95)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 96:136)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 137:159)
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 160:176)
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 177:189)
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 190:209)

-
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://pdbjlvh1.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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 326 molecules

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 326 molecules

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 326 molecules

-
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