PDB-5dlc: X-ray Crystal Structure of a Pyridoxine 5-prime-phosphate synthas...

ID or keywords:

Entry

Database: PDB / ID: 5dlc

Title

X-ray Crystal Structure of a Pyridoxine 5-prime-phosphate synthase from Pseudomonas aeruginosa

Components

Pyridoxine 5'-phosphate synthase

Keywords

TRANSFERASE / SSGCID / Psuedomonas aeruginosa / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Fairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: X-ray Crystal Structure of a Pyridoxine 5-prime-phosphate synthase from Pseudomonas aeruginosa
Authors: Fairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Sep 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5dlc.cif.gz	378.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5dlc.ent.gz	312.9 KB	Display	PDB format
PDBx/mmJSON format	5dlc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5dlc_validation.pdf.gz	454.2 KB	Display	wwPDB validaton report
Full document	5dlc_full_validation.pdf.gz	458.3 KB	Display
Data in XML	5dlc_validation.xml.gz	34.4 KB	Display
Data in CIF	5dlc_validation.cif.gz	47.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlc ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlc	HTTPS FTP

-
Related structure data

Related structure data	3f4nS S: Starting model for refinement
Similar structure data	5tim-d 1qds-1 3gk0-5 1n55-1 3f4n-1 3g7n-d 6ooi-1 1trd-3 1rd5-d 2qy6-1 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: SSGCID-PsaeA.00131.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pyridoxine 5'-phosphate synthase

B: Pyridoxine 5'-phosphate synthase

C: Pyridoxine 5'-phosphate synthase

D: Pyridoxine 5'-phosphate synthase

hetero molecules

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

1

A: Pyridoxine 5'-phosphate synthase

B: Pyridoxine 5'-phosphate synthase

hetero molecules

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

2

C: Pyridoxine 5'-phosphate synthase

D: Pyridoxine 5'-phosphate synthase

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

Unit cell

Length a, b, c (Å)	150.460, 150.460, 86.570
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Pyridoxine 5'-phosphate synthase / PNP synthase Mass: 28331.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pdxJ / Plasmid: PsaeA.00131.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q02HS5, pyridoxine 5'-phosphate synthase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.5 Å³/Da / Density % sol: 50.72 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus A8: 0.06 M MgCl2, 0.06 M CaCl2, 0.1 M HEPES/MOPS pH 7.50, 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2015
Radiation	Monochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.65→50 Å / Num. all: 33092 / Num. obs: 32181 / % possible obs: 97.2 % / Redundancy: 3.21 % / R_sym value: 0.082 / Net I/av σ(I): 12.97 / Net I/σ(I): 12.97
Reflection shell	Resolution: 2.65→2.72 Å / Redundancy: 3.25 % / R_merge(I) obs: 0.382 / Mean I/σ(I) obs: 3.18 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10pre_2090: ???)	refinement
XDS		data reduction
XSCALE		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3F4N

3f4n

Resolution: 2.65→49.25 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2125	1647	4.98 %	RANDOM
R_work	0.1735	-	-	-
obs	0.1755	33065	99.92 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.65→49.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7377	0	5	195	7577

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7503
X-RAY DIFFRACTION	f_angle_d	0.719	10166
X-RAY DIFFRACTION	f_dihedral_angle_d	16.46	4594
X-RAY DIFFRACTION	f_chiral_restr	0.034	1167
X-RAY DIFFRACTION	f_plane_restr	0.003	1376

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 (%)
2.6501-2.728	0.3505	133	0.2622	2588	X-RAY DIFFRACTION	100
2.728-2.8161	0.2338	136	0.2356	2571	X-RAY DIFFRACTION	100
2.8161-2.9167	0.2717	136	0.2182	2595	X-RAY DIFFRACTION	100
2.9167-3.0335	0.2727	135	0.2105	2619	X-RAY DIFFRACTION	100
3.0335-3.1715	0.2665	134	0.2169	2575	X-RAY DIFFRACTION	100
3.1715-3.3387	0.2668	140	0.2184	2653	X-RAY DIFFRACTION	100
3.3387-3.5478	0.2172	138	0.178	2559	X-RAY DIFFRACTION	100
3.5478-3.8217	0.2037	137	0.1664	2620	X-RAY DIFFRACTION	100
3.8217-4.2061	0.196	140	0.1442	2608	X-RAY DIFFRACTION	100
4.2061-4.8142	0.162	137	0.1316	2660	X-RAY DIFFRACTION	100
4.8142-6.0637	0.1821	141	0.1505	2635	X-RAY DIFFRACTION	100
6.0637-49.2581	0.1559	140	0.1392	2735	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	2.2916	0.6665	0.5071	1.093	-0.4094	2.8696	-0.1004	0.2415	0.055	-0.029	0.0502	-0.0699	0.0159	-0.0223	-0.0005	0.22	-0.0216	-0.0273	0.1994	0.0103	0.2134	-54.2868	46.1249	30.3136
2	1.3767	0.4894	-1.103	1.0944	-0.4978	0.8777	-0.0238	0.2153	-0.1673	0.0341	0.1012	-0.053	0.0586	-0.1953	-0.0731	0.2836	-0.0589	-0.0253	0.2567	0.0055	0.217	-62.3076	37.5929	34.4924
3	1.5943	-0.7416	-1.347	1.5593	-0.9446	3.2548	0.3821	0.3204	0.3498	0.2413	0.1262	-0.1755	-1.027	-0.9201	-0.0603	0.3272	0.0222	0.0024	0.382	0.033	0.4627	-70.9137	53.8861	43.4917
4	1.2327	0.0022	0.6099	2.2712	0.7202	2.4437	0.1594	-0.2388	-0.0172	0.2208	-0.0749	0.1916	0.2259	-0.5465	-0.0715	0.2863	-0.075	0.0314	0.298	0.0408	0.2953	-69.5196	41.8068	47.0026
5	2.2781	0.7574	-0.3778	2.4947	0.227	1.6328	-0.0928	-0.1245	0.4358	-0.1393	0.1468	0.2006	0.01	-0.1964	-0.0446	0.2672	-0.0144	0.0167	0.2819	0.0412	0.3	-62.6539	52.9106	51.143
6	3.2528	2.1045	-0.7101	1.9758	-1.183	0.973	0.1512	-0.2669	0.2218	0.2681	-0.0471	0.0206	-0.063	0.1056	-0.1259	0.3135	-0.0563	0.0426	0.269	-0.0332	0.1919	-53.5104	54.3299	52.3939
7	1.0108	-0.6415	0.417	2.5086	-0.7457	3.9945	0.0839	0.0597	0.106	0.0498	-0.0586	0.0326	-0.0458	0.2683	0.0195	0.2188	-0.0281	-0.0069	0.2758	0.0124	0.2135	-44.3061	50.8789	38.5642
8	1.8504	0.299	-1.2023	1.3735	0.166	3.0998	0.0402	0.4256	-0.0229	-0.0537	-0.1029	0.2473	-0.5483	-0.6734	-0.0741	0.1649	-0.0162	0.0082	0.2344	0.0235	0.2285	-47.8231	62.6605	22.4302
9	0.3858	0.4756	-0.7124	1.9824	-0.7263	1.9036	-0.0151	0.1696	-0.1951	-0.067	0.046	0.1723	-0.1137	-0.0055	-0.0474	0.1664	-0.0242	-0.0003	0.2597	-0.0203	0.2717	-48.0032	66.747	20.4085
10	0.9371	0.6982	-0.0147	0.5745	0.2971	2.3525	-0.0904	0.0977	0.1482	-0.0712	0.0012	0.2051	-0.1945	-0.307	0.0503	0.2093	0.0337	-0.0027	0.2601	0.0534	0.368	-52.9154	73.2438	13.2917
11	1.6079	0.4922	-0.1334	2.8149	1.0866	1.6292	-0.087	0.5924	0.306	-0.5395	0.1378	0.3121	-0.3333	-0.1875	-0.0225	0.3404	-0.0348	0.0142	0.422	0.1535	0.3344	-54.3984	75.1125	2.0022
12	1.6299	-1.226	-0.2778	2.6506	0.3775	1.8106	0.0647	0.5563	0.0663	0.0128	-0.0504	0.4428	0.1455	-0.2637	0.0514	0.3041	-0.0995	-0.0447	0.4818	0.1171	0.3153	-53.2578	62.089	-1.2129
13	1.8701	0.2054	0.0149	2.3651	-0.4882	1.1008	0.0487	0.6679	-0.2135	-0.6027	-0.0823	-0.0684	0.328	-0.0993	0.012	0.3403	-0.0365	-0.0381	0.6225	-0.0454	0.2736	-48.8384	54.5778	-4.8772
14	0.5659	0.1127	-0.2855	1.213	-1.0924	1.0253	-0.1716	0.4607	-0.2279	-0.1068	0.229	-0.103	0.1389	-0.308	0.0147	0.2555	-0.065	-0.0258	0.3249	0.0338	0.253	-46.1174	58.0723	5.1211
15	1.5727	-0.2542	0.5854	4.9941	1.4247	0.6842	0.2875	0.5032	-0.1815	-0.1527	-0.4095	-0.6669	-0.4448	0.2439	0.1111	0.3132	-0.0803	0.0712	0.3021	-0.0147	0.2592	-40.5798	55.6766	1.2366
16	1.4641	-0.2849	0.0049	0.6671	-0.2421	2.2034	0.0153	-0.0455	-0.0075	0.2043	-0.2403	-0.0935	-0.0421	-0.0338	0.0684	0.1899	-0.0353	-0.0436	0.3027	0.0055	0.2266	-44.7508	55.1942	17.8206
17	3.6138	-0.5314	-0.8259	3.8585	0.5908	2.7407	-0.0247	0.0068	-0.2212	-0.1048	0.1199	0.0853	-0.0208	0.1922	-0.1477	0.1906	-0.043	-0.0238	0.249	0.0195	0.2835	-36.2051	54.7433	13.6337
18	1.9278	-0.0644	0.0365	1.792	0.6667	2.6989	-0.4023	-0.0785	-0.4811	0.1326	0.0922	-0.6015	0.108	0.4198	0.0374	0.3	0.067	0.0293	0.2296	0.0297	0.3882	-7.173	36.3099	26.9808
19	1.4204	0.2614	0.7085	1.8529	-0.1875	2.4195	0.1069	-0.2428	-0.4599	-0.0374	-0.0217	-0.1797	0.2464	0.0604	0.0425	0.284	0.0407	0.0668	0.2701	0.0483	0.4611	-6.5664	32.5676	23.6539
20	1.8118	-0.3743	-0.7124	0.1262	-0.0536	1.17	-0.1197	0.2446	-0.434	-0.2939	0.0319	-0.4835	0.4393	0.1336	0.0999	0.369	0.087	0.1181	0.288	-0.0018	0.5581	-4.0812	24.1979	18.6181
21	2.191	1.1447	0.3032	1.854	-0.2462	3.218	-0.0461	-0.1017	-0.204	-0.4766	-0.3184	-0.5072	0.3917	0.7136	0.021	0.4502	0.0469	0.1641	0.4019	-0.0792	0.7148	11.864	35.3623	13.498
22	0.4213	0.4511	0.0987	0.9098	0.0803	0.0318	-0.0753	0.1729	-0.182	-0.2681	0.1907	-0.4349	0.1369	0.2981	-0.2751	0.3815	0.1858	0.2854	0.2407	-0.3716	0.7884	7.1785	23.224	6.8054
23	0.1734	0.1186	-0.4194	0.0959	-0.3569	1.2961	0.117	0.5374	-0.0313	0.0323	0.0221	0.1561	-0.0656	-0.1427	-0.0874	0.5197	0.0237	0.1691	0.2783	-0.0647	0.5449	2.1164	34.0054	7.3243
24	1.5083	-0.6459	0.4932	1.714	0.0045	0.848	-0.2404	0.1914	-0.3911	-0.0122	0.4587	-0.214	0.1277	0.3459	-0.111	0.4042	-0.044	0.178	0.4882	-0.1393	0.4869	4.6961	41.09	6.1023
25	2.0561	0.6141	-0.0738	1.4659	-0.6037	0.6445	-0.1071	0.3166	-0.0772	-0.6127	0.1017	-0.5502	-0.1339	0.3059	-0.0911	0.3994	0.0422	0.167	0.4445	0.0076	0.3072	1.7941	49.6632	2.4969
26	1.3851	-0.1879	-0.6279	1.9599	0.4126	1.3381	-0.0434	0.2151	-0.3093	-0.3042	-0.0187	0.0256	0.1276	0.073	0.0838	0.3387	-0.0157	0.0907	0.3118	-0.0643	0.297	-5.8109	44.9984	8.2332
27	1.9044	-0.0452	0.1527	1.2598	-0.3124	2.3124	-0.0306	0.1921	-0.1779	-0.0163	0.0234	-0.2228	0.0897	0.1736	-0.0314	0.2554	0.0071	0.0248	0.298	0.0169	0.3175	-12.7982	45.1277	19.0105
28	1.8124	0.8622	-0.7234	1.5913	0.0845	2.2446	-0.0857	-0.0697	-0.2437	0.1144	-0.1171	-0.2257	0.0862	0.4379	0.1992	0.2177	0.0084	0.0156	0.3775	0.0596	0.2918	-3.8811	51.14	38.202
29	2.0775	-0.078	-0.0675	1.926	0.4695	1.8713	0.2171	-0.0481	-0.2581	0.1	-0.3376	-0.2791	-0.1415	0.4076	-0.0038	0.283	-0.0401	-0.0163	0.4164	0.0486	0.2254	-0.3894	58.5266	43.2574
30	1.4279	0.6793	-0.642	0.8568	-0.1696	0.3278	0.1163	-0.1839	-0.442	0.1971	-0.1107	-0.7414	0.0052	0.7115	0.0345	0.3159	-0.0863	-0.0662	0.6943	0.1366	0.4264	5.7888	59.2268	49.6429
31	1.4174	2.545	-1.0489	4.6668	-2.1696	1.8352	-0.1255	-0.5663	-0.8595	-0.3601	-0.2485	-0.6073	0.3046	0.8264	-0.1329	0.3504	0.0734	-0.0771	0.7293	0.2398	0.5688	8.5661	41.4323	53.6473
32	1.0008	-0.3259	-1.1302	1.6354	0.2459	1.2644	-0.0001	-0.5294	0.0022	0.5075	0.3766	-0.3318	-0.2043	0.2567	0.9141	0.399	-0.0707	-0.2278	0.793	0.1613	0.4577	5.3501	51.8553	58.9775
33	1.6089	-0.5048	0.0228	1.0203	-0.113	1.1206	-0.1231	-0.4737	-0.4937	0.3036	0.0022	-0.304	-0.0566	0.3711	-0.0925	0.4652	-0.0345	-0.1474	0.6461	0.1721	0.4229	-1.9869	41.0523	59.0668
34	1.3912	-0.3555	0.2612	0.592	0.3895	1.0903	0.1273	-0.4914	-0.5538	0.3934	-0.2602	0.0085	0.3117	0.2914	-0.3438	0.4587	-0.0273	-0.1101	0.6756	0.2762	0.2879	-9.537	38.3969	57.7489
35	2.117	2.0034	0.8091	4.247	1.2621	0.4118	-0.1632	-0.6568	-0.2604	0.4692	-0.0827	0.1932	-0.4068	0.3154	0.0605	0.4027	-0.004	-0.0605	0.4755	0.062	0.2983	-15.9099	42.2957	56.433
36	1.0569	-0.1274	-0.0787	0.6877	-0.9182	1.2716	-0.1631	-0.0435	-0.0858	-0.0893	-0.1324	-0.1795	-0.203	0.0876	0.1996	0.2228	0.0243	0.0117	0.3144	0.0783	0.3418	-11.5987	43.7545	39.9823
37	2.8737	0.4015	-1.4787	1.49	0.5106	1.7343	0.0454	0.0258	0.0616	0.0122	-0.084	0.2835	-0.1114	0.6578	0.2394	0.2399	-0.0317	-0.035	0.2799	0.062	0.3706	-19.5348	46.5853	44.4699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 65 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 66 through 105 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 120 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 121 through 148 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 149 through 175 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 176 through 221 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 222 through 254 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 13 through 37 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 38 through 65 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 120 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 121 through 148 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 149 through 175 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 176 through 195 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 196 through 210 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 211 through 221 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 222 through 237 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 238 through 254 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 13 through 37 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 38 through 65 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 66 through 104 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 105 through 120 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 121 through 137 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 138 through 148 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 149 through 175 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 176 through 195 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 196 through 221 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 222 through 254 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 13 through 65 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 66 through 87 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 88 through 104 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 105 through 120 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 121 through 148 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 149 through 175 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 176 through 210 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 211 through 221 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 222 through 237 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 238 through 254 )

-
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

-
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