PDB-3dfz: SirC, precorrin-2 dehydrogenase

ID or keywords:

Entry

Database: PDB / ID: 3dfz

Title

SirC, precorrin-2 dehydrogenase

Components

Precorrin-2 dehydrogenase

Keywords

OXIDOREDUCTASE / NAD dehydrogenase /

Cobalamin biosynthesis / NAD / Porphyrin biosynthesis

Function / homology

Function and homology information

precorrin-2 dehydrogenase /

precorrin-2 dehydrogenase activity / siroheme biosynthetic process /

ferrochelatase activity / cobalamin biosynthetic process
Similarity search - Function

Biological species

Bacillus megaterium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Schubert, H.L. / Hill, C.P. / Warren, M.J.

Citation

Journal: Biochem.J. / Year: 2008
Title: Structure and function of SirC from Bacillus megaterium: a metal-binding precorrin-2 dehydrogenase
Authors: Schubert, H.L. / Rose, R.S. / Leech, H.K. / Brindley, A.A. / Hill, C.P. / Rigby, S.E.J. / Warren, M.J.

History

Deposition	Jun 12, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 21, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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 / _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	3dfz.cif.gz	179.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3dfz.ent.gz	144.6 KB	Display	PDB format
PDBx/mmJSON format	3dfz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/df/3dfz ftp://data.pdbj.org/pub/pdb/validation_reports/df/3dfz	HTTPS FTP

-
Related structure data

Similar structure data	6gy4-d 3rea-d 1x86-4 3cta-1 5xtm-d 4hin-d 5hpl-2 4u7c-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Precorrin-2 dehydrogenase

B: Precorrin-2 dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	108.595, 108.595, 201.028
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-206- SO4
2	1	A-206- SO4
3	1	B-203- SO4
4	1	A-208- HOH

#1: Protein	Precorrin-2 dehydrogenase / / SirC Mass: 25536.162 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: sirC / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon* RIL / References: UniProt: P61818, precorrin-2 dehydrogenase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.92 % / Mosaicity: 0.266 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: (NH3)4SO4, MES, LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU MICROMAX-007 HF	1	1.54
SYNCHROTRON	NSLS	X29A		2	1.0772, 1.0723, 1.0540

Detector

Type	ID	Detector	Date	Details
RIGAKU RAXIS IV	1	IMAGE PLATE	Apr 11, 2004	mirros
ADSC QUANTUM 315	2	CCD	Jun 9, 2004

Radiation

ID	Monochromator	Protocol	Scattering type	Wavelength-ID	Monochromatic (M) / Laue (L)
1	Veri-max	SINGLE WAVELENGTH	x-ray	1
2	Si(111)	MAD	x-ray	1	M

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.54	1
2	1.0772	1
3	1.0723	1
4	1.054	1

Reflection

Redundancy: 8.5 % / Av σ(I) over netI: 9.5 / Number: 171627 / R_merge(I) obs: 0.098 / Χ²: 1.94 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 20204 / % possible obs: 98.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.95	50	100	1	0.077	6.091	8.7
3.93	4.95	100	1	0.066	2.906	9.1
3.44	3.93	100	1	0.076	2.098	9.2
3.12	3.44	100	1	0.094	1.489	9.3
2.9	3.12	100	1	0.134	1.229	9.3
2.73	2.9	100	1	0.198	1.048	9.1
2.59	2.73	99.6	1	0.259	0.938	8.4
2.48	2.59	95	1	0.302	0.909	7.6
2.38	2.48	94.4	1	0.362	0.839	7.2
2.3	2.38	98	1	0.46	0.787	6.7

Reflection

Resolution: 2.3→99 Å / Num. obs: 20508 / % possible obs: 99.4 % / R_merge(I) obs: 0.062 / Χ²: 1.079 / Net I/σ(I): 18.1

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.3-2.38	0.352	1924	1.069	1,2	94.7
2.38-2.48	0.309	2038	1.05	1,2	100
2.48-2.59	0.252	2038	1.094	1,2	100
2.59-2.72	0.202	2028	1.135	1,2	100
2.72-2.9	0.151	2043	1.112	1,2	100
2.9-3.12	0.097	2051	1.087	1,2	100
3.12-3.43	0.065	2066	1.083	1,2	100
3.43-3.93	0.049	2077	1.044	1,2	100
3.93-4.95	0.039	2092	1.084	1,2	100
4.95-99	0.037	2151	1.03	1,2	98.8

-
Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	1.0772	9.58	-6.95
1	3 wavelength	2	1.0723	5.35	-19.65
1	3 wavelength	3	1.054	6.07	0.04

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Pt	1	0.438	0.398	0.137	0.041
2	Pt	51.56	0.915	0.581	0.044	0.463

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.03	phasing
RESOLVE		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
ADSC	Quantum	data collection

Refinement

Method to determine structure:

MAD / Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.903 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.795 / SU B: 14.462 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27466	1050	5.1 %	RANDOM
R_work	0.21089	-	-	-
obs	0.21411	19447	99.65 %	-

Solvent computation

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

Displacement parameters

B_iso max: 96.37 Å² / B_iso mean: 25.19 Å² / B_iso min: 19.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.66 Å²	-0.83 Å²	0 Å²
2-	-	-1.66 Å²	0 Å²
3-	-	-	2.48 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3163	0	36	204	3403

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	3266
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.398	1.974	4404
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.846	5	399
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.496	24.258	155
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.201	15	626
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.2	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	505
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2383
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.639	1.5	1971
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.211	2	3194
X-RAY DIFFRACTION	r_scbond_it	1.883	3	1295
X-RAY DIFFRACTION	r_scangle_it	3.041	4.5	1207
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	84	-
R_work	0.241	1344	-
all	-	1428	-
obs	-	-	95.84 %

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	3.6306	-0.0266	0.6096	3.5998	-0.621	2.4401	-0.0006	0.0603	-0.0269	0.0014	0.0328	-0.1005	-0.0067	0.1943	-0.0321	0.2015	0.003	0.0175	0.2008	0.0012	0.2279	11.752	35.4933	85.4781
2	2.5543	-0.2375	-0.5242	2.6528	0.3015	1.7955	-0.006	0.055	0.0507	-0.0298	0.0582	0.0871	0.0156	-0.1326	-0.0523	0.2349	0.0011	-0.0303	0.2524	-0.0194	0.2453	27.1122	40.1491	87.062
3	2.6948	-0.7087	0.5562	2.2884	-0.8979	1.6446	-0.0374	-0.243	-0.0061	0.2757	0.0567	0.2222	-0.0968	-0.1882	-0.0194	0.2504	-0.0082	-0.003	0.2417	-0.0085	0.2454	24.4576	43.011	90.6154
4	0.0027	-0.0846	-0.0302	2.6099	0.932	0.3328	0.0413	0.0928	0.0206	-0.1506	-0.0124	-0.0792	-0.0274	0.0309	-0.0288	0.2476	0.0006	-0.0024	0.2556	0.003	0.248	35.8555	46.9338	88.8085
5	3.0627	-0.7071	-1.3666	2.0553	1.4048	2.1503	-0.0493	-0.1325	-0.1035	0.2287	-0.0303	0.2654	0.0507	-0.1444	0.0797	0.2955	-0.0015	-0.011	0.2988	0.0089	0.2828	34.9458	43.2924	94.71
6	2.7493	-1.5105	0.7709	1.3011	0.0899	0.777	-0.0019	0.0133	0.005	-0.0484	-0.0114	-0.1388	0.021	0.1696	0.0134	0.2389	-0.0053	-0.0029	0.2235	-0.0093	0.2207	31.5633	30.6949	87.2897
7	0.4924	-0.8585	0.194	1.501	-0.4062	1.1315	-0.0275	0.2497	0.1644	-0.312	0.0194	-0.0907	-0.0991	0.0598	0.0082	0.3166	-0.0011	-0.0009	0.3249	-0.003	0.3194	33.652	30.3174	76.8642
8	2.2363	-1.2362	0.1629	4.1545	-0.1172	0.6054	0.037	0.1706	-0.0651	-0.2795	-0.0726	-0.1845	0.1817	0.1724	0.0357	0.2299	-0.0062	-0.0007	0.2417	-0.0069	0.225	22.1967	29.1876	81.285
9	2.2066	-0.4162	-0.6823	1.5755	1.1615	3.0155	-0.0261	-0.0985	-0.0257	0.0579	-0.0033	0.0247	0.0321	0.0291	0.0294	0.1472	-0.0044	-0.0046	0.1403	0.0055	0.1613	11.4488	47.0438	86.9415
10	2.7754	0.0714	-0.5309	1.6626	0.1145	3.0707	0.0231	0.0969	-0.0439	-0.0842	0.0356	-0.1129	0.0195	0.0908	-0.0588	0.1505	0.0018	-0.0079	0.1576	0.016	0.1622	12.4978	52.7005	76.5144
11	3.7724	0.645	-0.4509	1.112	1.3211	2.0053	-0.0013	-0.0885	-0.0706	-0.0127	-0.077	-0.1202	0.0833	0.1519	0.0782	0.1401	0.0096	-0.0038	0.1395	-0.0163	0.1525	5.6982	51.7447	97.6728
12	2.5911	-0.1839	-0.2834	0.0688	0.0134	0.0318	-0.0068	-0.0418	-0.3059	0.0068	0.0081	0.1939	0.218	-0.193	-0.0013	0.2329	-0.0009	-0.0009	0.2226	-0.0012	0.2255	-6.5322	38.473	106.4836
13	1.5138	-0.2254	-0.1187	2.408	-1.073	2.0614	-0.0216	0.0107	-0.0426	-0.0333	0.0656	0.3463	0.1474	-0.2359	-0.0441	0.1735	0.0065	0.0002	0.1877	-0.0069	0.1712	-7.6121	49.2016	100.5603
14	0.8278	-0.0647	0.0632	0.9516	-0.0535	1.1642	-0.0072	-0.1199	-0.1146	0.108	-0.0055	0.0387	0.114	-0.0485	0.0126	0.1446	0.0012	-0.0013	0.1462	-0.0021	0.1494	-1.2383	55.3963	106.274
15	1.4417	-1.1444	-1.7223	6.8847	-1.4639	3.5426	0.0697	-0.432	-0.1916	0.4626	-0.0431	-0.1379	0.206	0.0064	-0.0267	0.2213	0.0016	0.0011	0.2335	-0.0009	0.2255	-6.3639	46.5426	114.1053
16	0.8078	0.7578	0.1506	2.2268	0.3051	0.6752	-0.0009	0.0388	-0.0619	-0.0377	0.0174	-0.0176	0.0676	-0.0196	-0.0165	0.1822	0.0116	-0.009	0.199	0.0067	0.1898	11.4175	29.1323	82.2961
17	1.375	0.7853	-0.2212	0.591	-0.5118	1.0787	0.0199	-0.0207	0.1883	0.0199	-0.0041	0.053	-0.1911	-0.04	-0.0158	0.2852	0.003	-0.0007	0.2827	-0.0007	0.2857	-3.1879	27.9604	83.0069
18	1.3263	-0.0958	0.1794	1.0051	0.0304	0.594	0.0162	0.0123	0.094	0.0375	0.0273	0.2319	-0.0646	-0.1889	-0.0434	0.2005	0.0017	-0.0006	0.1964	-0.0049	0.1925	-0.396	21.0705	76.6179
19	1.3132	1.0841	-3.5047	0.895	-2.8932	9.3536	0.0244	-0.5089	-0.3113	0.3556	0.0672	0.1321	0.252	-0.1827	-0.0917	0.2528	0.0016	-0.0029	0.2307	-0.009	0.2579	-1.3553	11.9839	85.0303
20	3.4647	-0.0844	-1.0829	0.0021	0.0264	0.3385	0.0033	0.0381	-0.1901	-0.0105	-0.0135	-0.0913	0.1832	0.1152	0.0102	0.3654	-0.0007	-0.0022	0.3597	-0.0018	0.3593	8.6418	12.6946	90.6785
21	0.8044	1.5861	0.82	5.0034	-1.1105	4.7998	-0.1447	-0.0976	-0.4079	0.1625	0.0257	0.0861	0.2773	0.0049	0.119	0.2495	-0.0136	-0.0247	0.2147	-0.0031	0.2114	8.0538	22.8297	86.9249
22	0.5001	-0.2663	0.7828	1.502	-0.0795	1.3091	0.0033	-0.0415	-0.0237	0.0272	0.0056	0.1036	-0.0134	-0.1086	-0.0089	0.3862	-0.0025	-0.0006	0.3706	-0.0005	0.371	3.3126	20.3437	97.2181
23	3.5491	-0.6857	0.0996	4.7349	-0.5848	2.8596	-0.1154	-0.5674	-0.1503	0.4148	0.0797	-0.4292	0.1839	0.3949	0.0357	0.2679	-0.0068	0.0036	0.2516	-0.0054	0.2424	11.9366	26.2692	91.9424
24	0	0	0	0	0	0	0.0038	-0.2057	0.1147	0.1834	-0.0433	0.2414	-0.0066	-0.2548	0.0394	0.3034	0	0	0.3034	0	0.3034	2.5372	31.1669	96.8463
25	0.4624	-0.1158	-0.377	0.5284	0.1899	0.3256	-0.0079	-0.0457	-0.0682	0.0449	0.0156	0.0076	0.0842	-0.0046	-0.0077	0.1652	-0.0052	-0.0031	0.1697	-0.0024	0.1756	2.9944	42.3526	85.0748
26	1.285	0.0097	1.1036	2.6149	-2.1169	2.6751	0.0371	-0.0079	0.1728	0.0454	-0.0029	0.2138	-0.2306	-0.235	-0.0342	0.1797	0.0001	0.0017	0.1835	-0.0055	0.1882	-2.6329	51.0563	83.9275
27	0.2399	0.2511	0.5777	1.2495	0.2244	1.5379	-0.0426	0.0354	-0.102	-0.0304	0.0028	-0.0226	0.1104	0.0305	0.0398	0.151	-0.0007	-0.0051	0.1453	0.0046	0.154	5.0039	50.7351	66.8044
28	3.5795	1.5539	-0.8094	0.8839	-0.5969	0.4711	-0.0372	0.1525	-0.0872	-0.1072	0.0554	-0.4398	-0.0831	0.3646	-0.0182	0.299	0.0092	-0.0039	0.2877	0.0017	0.2905	22.1869	49.8556	59.2109
29	0.6603	-0.0071	0.0611	1.1685	0.1206	2.0468	0.0024	0.0164	0.0144	0.0501	-0.0139	-0.334	0.1153	0.33	0.0116	0.1673	-0.0072	0.0031	0.1436	0.0021	0.1605	11.3947	58.3016	63.3456
30	4.5394	0.0036	-3.3607	1.0195	-0.3866	2.6326	-0.0512	0.443	-0.1533	-0.4698	0.0143	-0.6968	0.0948	0.6699	0.037	0.2943	0	-0.0071	0.2833	-0.0016	0.288	15.975	55.7338	52.4098

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	1 - 8	22 - 29
2	X-RAY DIFFRACTION	2	A	A	9 - 24	30 - 45
3	X-RAY DIFFRACTION	3	A	A	25 - 38	46 - 59
4	X-RAY DIFFRACTION	4	A	A	39 - 51	60 - 72
5	X-RAY DIFFRACTION	5	A	A	52 - 60	73 - 81
6	X-RAY DIFFRACTION	6	A	A	61 - 77	82 - 98
7	X-RAY DIFFRACTION	7	A	A	78 - 90	99 - 111
8	X-RAY DIFFRACTION	8	A	A	91 - 109	112 - 130
9	X-RAY DIFFRACTION	9	A	A	110 - 124	131 - 145
10	X-RAY DIFFRACTION	10	A	A	125 - 142	146 - 163
11	X-RAY DIFFRACTION	11	A	A	143 - 157	164 - 178
12	X-RAY DIFFRACTION	12	A	A	158 - 171	179 - 192
13	X-RAY DIFFRACTION	13	A	A	172 - 184	193 - 205
14	X-RAY DIFFRACTION	14	A	A	185 - 195	206 - 216
15	X-RAY DIFFRACTION	15	A	A	196 - 201	217 - 222
16	X-RAY DIFFRACTION	16	B	B	1 - 17	22 - 38
17	X-RAY DIFFRACTION	17	B	B	18 - 27	39 - 48
18	X-RAY DIFFRACTION	18	B	B	28 - 57	49 - 78
19	X-RAY DIFFRACTION	19	B	B	58 - 62	79 - 83
20	X-RAY DIFFRACTION	20	B	B	63 - 69	84 - 90
21	X-RAY DIFFRACTION	21	B	B	70 - 78	91 - 99
22	X-RAY DIFFRACTION	22	B	B	79 - 92	100 - 113
23	X-RAY DIFFRACTION	23	B	B	93 - 99	114 - 120
24	X-RAY DIFFRACTION	24	B	B	100 - 106	121 - 127
25	X-RAY DIFFRACTION	25	B	B	107 - 134	128 - 155
26	X-RAY DIFFRACTION	26	B	B	135 - 143	156 - 164
27	X-RAY DIFFRACTION	27	B	B	144 - 158	165 - 179
28	X-RAY DIFFRACTION	28	B	B	159 - 171	180 - 192
29	X-RAY DIFFRACTION	29	B	B	172 - 194	193 - 215
30	X-RAY DIFFRACTION	30	B	B	195 - 201	216 - 222

-
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