PDB-2xjm: Crystal structure of Streptococcus suis Dpr with cobalt

ID or keywords:

Entry

Database: PDB / ID: 2xjm

Title

Crystal structure of Streptococcus suis Dpr with cobalt

Components

DNA PROTECTION DURING STARVATION PROTEIN

Keywords

OXIDOREDUCTASE / IRON STORAGE / METAL-BINDING

Function / homology

Function and homology information

Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm
Similarity search - Function

Biological species

STREPTOCOCCUS SUIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.3 Å

Authors

Haikarainen, T. / Thanassoulas, A. / Stavros, P. / Nounesis, G. / Haataja, S. / Papageorgiou, A.C.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Structural and Thermodynamic Characterization of Metal Ion Binding in Streptococcus Suis Dpr.
Authors: Haikarainen, T. / Thanassoulas, A. / Stavros, P. / Nounesis, G. / Haataja, S. / Papageorgiou, A.C.

History

Deposition	Jul 6, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 24, 2010	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2011	Group: Database references / Version format compliance
Revision 1.2	Jul 24, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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	2xjm.cif.gz	732.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2xjm.ent.gz	615 KB	Display	PDB format
PDBx/mmJSON format	2xjm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2xjm_validation.pdf.gz	534.9 KB	Display	wwPDB validaton report
Full document	2xjm_full_validation.pdf.gz	557.7 KB	Display
Data in XML	2xjm_validation.xml.gz	72.6 KB	Display
Data in CIF	2xjm_validation.cif.gz	101.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xj/2xjm ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xjm	HTTPS FTP

-
Related structure data

Related structure data	2xjnC 2xjoC 2xkqC 1umn 2bw1 2cf7 2ux1 2v15 C: citing same article (ref.)
Similar structure data	2cf7-d 2xjo-d 6hvq-1 2xkq-d 2xjn-d 2iy4-2 6sev-1 1qgh-d 2bkc-1 2bk6-1 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
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (3) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: DNA PROTECTION DURING STARVATION PROTEIN

B: DNA PROTECTION DURING STARVATION PROTEIN

C: DNA PROTECTION DURING STARVATION PROTEIN

D: DNA PROTECTION DURING STARVATION PROTEIN

E: DNA PROTECTION DURING STARVATION PROTEIN

F: DNA PROTECTION DURING STARVATION PROTEIN

G: DNA PROTECTION DURING STARVATION PROTEIN

H: DNA PROTECTION DURING STARVATION PROTEIN

I: DNA PROTECTION DURING STARVATION PROTEIN

J: DNA PROTECTION DURING STARVATION PROTEIN

K: DNA PROTECTION DURING STARVATION PROTEIN

L: DNA PROTECTION DURING STARVATION PROTEIN

hetero molecules

226 kDa, 12 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)	104.960, 137.420, 141.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	DNA PROTECTION DURING STARVATION PROTEIN / DPS-LIKE PEROXIDE RESISTANCE PROTEIN Mass: 18641.014 Da / Num. of mol.: 12 / Fragment: RESIDUES 8-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS SUIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P0CB53, Oxidoreductases; Oxidizing metal ions

#1: Protein

DNA PROTECTION DURING STARVATION PROTEIN / DPS-LIKE PEROXIDE RESISTANCE PROTEIN

Mass: 18641.014 Da / Num. of mol.: 12 / Fragment: RESIDUES 8-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

STREPTOCOCCUS SUIS (bacteria) / Production host:

ESCHERICHIA COLI (E. coli)
References: UniProt: P0CB53, Oxidoreductases; Oxidizing metal ions

-
Non-polymers , 5 types, 829 molecules

#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Co
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.18 Å³/Da / Density % sol: 44 % Description: FRIEDEL_LAW=FALSE WAS USED DURING DATA PROCESSING, AND A TOTAL OF 169544 REFLECTIONS WERE COLLECTED.
Crystal grow	pH: 7.4 Details: 30 - 35 % (V/V) PEG 400, 0.2 M CACL2, 0.1 M HEPES-NAOH (PH 7.4)

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.60846
Detector	Type: MARRESEARCH MARMOSAIC / Detector: CCD / Date: Oct 10, 2008 / Details: VERTICALLY FOCUSSING
Radiation	Monochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.60846 Å / Relative weight: 1
Reflection	Resolution: 2.3→25 Å / Num. obs: 88486 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / B_iso Wilson estimate: 43.3 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 16.6
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.11 / Mean I/σ(I) obs: 7.4 / % possible all: 76.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.4.0078	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.3→24.91 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.921 / SU B: 14.448 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2403	4425	5 %	RANDOM
R_work	0.17671	-	-	-
obs	0.17986	84061	100 %	-

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 mean: 19.295 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.31 Å²	0 Å²	0 Å²
2-	-	-0.19 Å²	0 Å²
3-	-	-	0.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→24.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14438	0	83	802	15323

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	14955
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.289	1.95	20242
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.005	5	1830
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	44.628	25.087	745
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.857	15	2610
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.06	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	2197
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11383
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	0.57	1.5	9080
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.133	2	14558
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.155	3	5875
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.441	4.5	5684
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.301→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.28	257	-
R_work	0.2	4871	-
obs	-	-	100 %

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	3.4134	-1.545	-0.8199	4.2919	1.9495	5.004	0.0168	0.2091	-0.3655	0.1529	-0.182	0.0112	0.4143	0.0476	0.1652	0.2552	0.0417	-0.0371	0.1547	0.0872	0.2567	13.655	106.511	19.7433
2	0.1167	0.2301	-0.0407	0.746	0.6372	1.7737	0.0354	-0.11	0.0043	0.1067	-0.0447	0.0659	0.053	0.0367	0.0093	0.2295	0.0336	-0.04	0.1779	0.0559	0.1411	12.9663	127.9766	28.4327
3	1.0329	0.3611	-0.1096	1.1698	0.5095	1.2488	0.0299	-0.1436	-0.2067	0.2092	-0.0314	-0.0047	0.1576	-0.0368	0.0014	0.2453	0.0595	-0.0454	0.132	0.0789	0.2102	13.9333	113.7453	24.967
4	3.7198	-0.324	2.2369	2.5317	2.5864	5.596	0.082	0.0101	-0.5707	0.1345	-0.0774	-0.1824	0.465	0.3025	-0.0047	0.2721	0.0916	-0.0304	0.1263	0.0312	0.2963	22.2818	105.0624	10.4315
5	0.4601	0.9627	0.6515	2.0147	1.3843	1.5932	-0.0353	-0.0281	-0.1813	0.0789	0.0301	-0.2325	0.0456	0.2896	0.0052	0.1884	0.0672	-0.0535	0.1671	0.0502	0.1977	26.5829	121.808	20.1451
6	2.7985	3.5861	2.7459	12.7313	0.9007	8.1437	0.0917	0.3568	0.1485	-0.4857	-0.0592	0.7173	-0.245	-0.4868	-0.0325	0.2769	-0.0044	-0.001	0.314	0.0105	0.2434	-6.1122	149.8765	-38.0122
7	0.429	-0.1432	-0.3058	0.8689	0.6012	2.0742	0.0152	0.0924	0.0242	-0.0561	0.0252	-0.0184	0.0597	0.0413	-0.0404	0.1235	-0.005	-0.0177	0.1885	0.0305	0.1707	-4.2556	158.8707	-15.2505
8	0.8748	-0.5096	-0.3209	1.2192	0.7564	1.226	0.0458	0.2722	0.148	-0.2613	-0.0652	0.0458	-0.1866	-0.0838	0.0193	0.1384	-0.0159	-0.0201	0.2296	0.0697	0.1205	-1.8835	161.2979	-25.4068
9	2.0153	-0.2758	0.5655	2.9442	4.1574	6.3291	-0.0583	0.2654	0.2633	-0.354	0.1291	-0.1236	-0.3458	0.2153	-0.0709	0.1475	0.018	-0.0188	0.1851	0.0442	0.2075	-13.7412	163.3948	-16.842
10	1.5125	-0.8394	-1.215	2.0471	1.0695	1.9758	0.0318	0.3199	-0.1049	-0.3049	-0.111	0.1892	-0.0382	-0.1702	0.0792	0.1229	-0.0076	-0.0636	0.1956	0.0254	0.1556	-14.8945	150.2947	-23.0014
11	1.0099	0.2866	0.4515	1.5224	0.7293	2.0822	0.0189	-0.0597	-0.1476	0.1036	0.0732	0.0932	-0.0082	0.1043	-0.092	0.2189	0.0061	0.0214	0.1382	0.0772	0.211	-3.6541	116.242	20.4515
12	0.5316	0.1196	0.3079	1.9556	0.9845	1.295	0.003	-0.1154	-0.2299	0.2632	0.0401	0.1289	0.26	-0.0216	-0.0431	0.2769	0.0034	0.0274	0.1613	0.1142	0.1906	-0.8809	114.5362	30.1003
13	4.6003	0.8777	-0.5732	8.4668	6.4723	6.4575	-0.1965	0.0881	-0.4051	0.2205	0.1561	0.2918	0.4437	-0.0752	0.0404	0.2679	-0.0212	0.0071	0.1988	0.075	0.28	-12.2234	109.3526	18.6625
14	0.9401	-0.1555	0.449	6.8539	4.5527	3.883	0.1766	-0.4076	0.074	0.6672	-0.0493	0.1108	-0.0355	-0.3593	-0.1273	0.325	-0.0191	0.1261	0.2301	0.1146	0.1571	-14.0225	124.683	34.1563
15	1.5957	1.6317	2.1562	1.9165	2.0271	3.5764	0.0395	-0.2162	-0.0996	0.1045	-0.0326	0.2607	0.0712	-0.265	-0.0069	0.2055	-0.0031	0.063	0.1741	0.0885	0.2392	-16.0594	122.2196	21.2298
16	4.0377	-1.7199	2.186	0.9703	0.1548	6.1454	-0.0435	-0.5614	0.7744	0.6167	-0.0485	-0.0592	-0.8598	0.0001	0.0919	0.2647	-0.0232	-0.0107	0.1999	0.021	0.2898	12.8867	179.3141	-6.7751
17	0.2611	-0.4891	-0.1334	2.5582	0.9388	0.9758	0.0139	0.1383	0.0214	-0.0308	-0.0865	0.0288	0.0631	0.001	0.0726	0.1078	-0.0239	0.0103	0.1951	0.0258	0.1263	12.518	154.7876	-19.6741
18	0.5201	-0.4087	-0.3965	1.2426	1.0312	1.3842	0.024	0.2413	0.135	-0.294	-0.0162	-0.0921	-0.1838	0.0839	-0.0078	0.136	-0.0244	0.0134	0.1976	0.0733	0.1609	9.862	165.1703	-21.2762
19	1.2301	-0.7108	-0.8408	5.4013	3.9454	5.3579	0.0503	0.0856	0.209	-0.3498	-0.0362	-0.2474	-0.3566	0.0574	-0.0142	0.0936	-0.0397	0.0137	0.1842	0.0741	0.1758	21.1978	165.4887	-15.24
20	1.2331	-1.6933	-0.7412	3.0332	1.6323	1.289	0.0275	0.1031	0.0965	-0.0542	-0.0113	-0.1735	0.0088	0.1345	-0.0161	0.1187	-0.0289	0.0039	0.2071	0.0447	0.1784	24.3831	157.9803	-12.078
21	3.5327	0.6159	0.5445	0.553	-0.2977	0.9022	-0.0329	0.211	-0.351	-0.1206	0.0771	-0.0578	0.2822	0.0786	-0.0441	0.2826	0.0365	-0.0047	0.1196	-0.1083	0.2332	7.4642	109.3869	-15.4863
22	4.6642	-0.4279	-0.6385	0.3407	0.3131	0.7605	0.0788	0.1982	-0.0158	-0.0886	0.0368	-0.0472	0.1249	0.0007	-0.1156	0.2564	0.0152	-0.0239	0.1213	-0.0234	0.2474	-0.2721	114.5166	-7.5583
23	0.5904	-0.1983	0.0809	0.4999	-0.2836	0.601	0.0604	0.2263	-0.4047	-0.2181	-0.0025	0.0665	0.3674	0.022	-0.0579	0.3371	0.0229	0.0002	0.1611	-0.1379	0.2658	8.0968	107.8449	-18.1158
24	6.4625	1.2173	0.4009	1.4646	-0.0469	1.5214	-0.1186	0.166	-0.602	-0.1881	0.1011	-0.1944	0.2947	0.2273	0.0175	0.3203	0.0991	-0.0021	0.0698	-0.1085	0.2966	15.3181	104.0735	-7.0097
25	2.7097	0.5485	-2.126	0.7158	-0.4263	1.6681	0.0131	-0.285	-0.3596	-0.0658	-0.0219	-0.024	0.1965	0.0735	0.0088	0.2837	0.0314	-0.0433	0.1386	-0.0224	0.2845	7.5697	105.7634	0.4099
26	6.9514	4.1648	-3.8947	4.8079	-0.3882	8.0055	0.1138	0.11	0.8659	-0.0457	-0.0574	-0.2095	-0.4767	-0.0396	-0.0564	0.269	-0.0092	-0.0151	0.26	-0.0162	0.2846	21.2507	172.8335	20.8933
27	1.6381	0.2701	0.5561	0.636	0.1273	0.9912	-0.007	-0.133	0.0785	0.1719	0.0106	0.0277	-0.0447	-0.048	-0.0036	0.1746	0.0299	0.0118	0.1156	-0.0143	0.1555	-3.4346	164.2758	16.5292
28	8.7188	-0.0335	3.1954	0.7321	0.4039	1.8802	0.0621	-0.1138	-0.2089	0.0868	-0.0198	-0.1069	0.0958	0.045	-0.0423	0.2105	-0.0007	0.0073	0.1786	-0.0013	0.194	3.668	159.6394	12.9439
29	1.5835	0.1145	0.0615	0.5254	-0.2824	0.4816	-0.007	-0.2567	0.3266	0.2626	-0.0121	-0.0067	-0.2355	-0.0639	0.0191	0.2551	-0.0007	-0.0334	0.1416	-0.0412	0.1338	7.4362	167.0579	24.6153
30	2.0862	-0.5322	0.1427	0.6897	-0.2828	0.731	-0.0508	-0.0452	0.1839	0.1449	0.0251	-0.0347	-0.1695	0.0469	0.0257	0.1661	-0.0078	-0.0143	0.1122	-0.0044	0.1942	5.9476	171.1558	8.6158
31	0.0277	-0.1418	-0.0155	1.1195	-0.5377	0.9773	0.0306	0.1587	-0.3328	-0.1722	0.0001	0.0091	0.1772	-0.0251	-0.0307	0.3129	0.0428	0.0195	0.2516	-0.1385	0.1717	6.9415	120.8315	-26.1162
32	8.1667	2.6097	0.2733	1.1877	0.0836	0.0092	0.181	-0.2565	-0.1123	0.0109	-0.149	0.0311	0.1534	-0.0216	-0.032	0.2302	0.0014	-0.0039	0.2013	-0.0607	0.1212	6.0251	126.8651	-20.0118
33	1.662	0.6866	-0.6775	1.2378	-0.4637	0.9248	-0.0073	0.3557	-0.3192	-0.4019	0.0559	-0.0336	0.37	0.103	-0.0486	0.3659	0.0213	-0.0204	0.2521	-0.1532	0.1604	5.0761	115.7662	-28.0837
34	8.3387	0.9866	-0.2421	0.8062	0.1178	1.4476	-0.0022	0.3526	-0.1628	-0.4067	0.0076	0.0395	0.224	-0.0526	-0.0054	0.2869	0.0021	-0.0256	0.2546	-0.0776	0.0827	0.8639	127.4796	-33.1816
35	5.4823	1.5	-1.258	1.6516	-0.5759	0.3984	-0.024	0.2255	0.0289	-0.1976	0.0598	0.1749	0.1149	-0.0135	-0.0358	0.2222	-0.0018	-0.0276	0.2408	-0.0651	0.069	0.0522	134.0312	-29.4486
36	6.1405	-0.9598	-0.8364	3.2617	1.4779	4.1977	-0.1139	-0.3443	0.2384	0.3516	-0.0484	0.4536	0.0096	-0.5166	0.1623	0.2771	0.0512	0.0673	0.1974	-0.0328	0.087	-11.0435	155.6853	32.6419
37	1.7533	-0.9889	-0.2003	1.7068	-0.301	0.1779	-0.0376	-0.1104	0.0837	0.1257	0.0101	-0.2094	-0.0192	0.0405	0.0275	0.2677	0.0008	-0.0402	0.1992	-0.0091	0.1324	13.9782	150.8227	27.2756
38	2.1832	-0.2503	0.1554	0.7933	-0.3388	0.1499	-0.0507	-0.2047	0.1387	0.313	0.0228	-0.0044	-0.0987	0.034	0.028	0.2931	0.0309	0.0239	0.1988	-0.0321	0.0873	0.6712	156.0783	30.0952
39	7.4552	-0.1669	0.9425	1.5526	-0.033	1.4479	-0.0633	-0.3553	0.3644	0.2404	0.0416	0.2504	-0.0771	-0.224	0.0217	0.3248	0.0329	0.0465	0.2357	0.0012	0.1404	-6.5797	147.3849	36.7732
40	3.4393	-1.3185	0.8587	0.9981	-0.3136	0.4706	-0.0216	-0.2065	-0.2289	0.3117	0.074	0.0439	-0.051	-0.0489	-0.0523	0.3027	-0.0036	0.0342	0.1955	0.0269	0.071	-0.4773	140.4164	33.5452
41	2.9347	0.7846	-1.1209	2.5496	-0.9101	2.705	0.0193	-0.246	-0.4861	0.2903	-0.018	-0.1199	0.2315	0.4218	-0.0013	0.131	0.0841	-0.0182	0.2555	0.0253	0.281	39.2514	126.4508	4.4141
42	1.6082	0.6532	0.2803	1.4343	-0.5799	1.0501	-0.0032	-0.0201	-0.1171	0.0445	-0.037	-0.0801	0.0795	0.0758	0.0402	0.1583	0.0317	0.0186	0.2074	-0.0135	0.1878	29.6058	139.427	-10.2463
43	0.309	0.1216	0.0656	1.5573	-1.0972	1.9828	-0.0005	0.0717	-0.0296	0.0418	-0.077	-0.2924	0.0476	0.2915	0.0775	0.1358	0.0651	-0.0199	0.2555	0.0152	0.2642	39.3403	132.2932	2.9678
44	2.3079	0.084	-0.4151	5.869	-3.8032	5.482	-0.029	-0.0437	-0.3209	0.0738	-0.1397	-0.3275	0.2498	0.4811	0.1687	0.1309	0.105	0.0538	0.2528	-0.0468	0.2445	36.9216	124.0111	-6.995
45	1.2644	0.2811	0.4993	1.3288	-1.5572	6.1234	-0.0046	0.0804	-0.2285	-0.0834	0.0028	-0.1137	0.3646	0.2449	0.0019	0.1892	0.0816	0.0325	0.1974	-0.0512	0.2567	30.1257	121.0819	-7.501
46	3.0404	-3.2325	3.1814	7.1114	-3.4601	3.3306	-0.1258	-0.7511	-0.3429	0.6087	0.2299	-0.0044	0.397	-0.3535	-0.1042	0.2837	-0.0106	0.0758	0.3581	0.053	0.3288	-31.7259	128.603	23.74
47	0.2198	0.0922	0.0158	1.0011	-0.5486	0.826	-0.0721	-0.0543	-0.0487	-0.0017	0.0839	0.1232	0.0962	-0.0615	-0.0118	0.1146	0.0208	0.0212	0.1693	0.0158	0.2258	-24.7192	147.3325	2.4683
48	1.3905	0.7863	-0.8315	7.6758	-4.9162	3.9506	-0.0624	0.0773	-0.2184	-0.2109	-0.0024	-0.1709	0.321	0.1865	0.0648	0.1736	0.0035	0.0296	0.2019	0.0015	0.2055	-19.0491	142.1604	7.4011
49	0.5156	0.1115	-0.0425	2.4208	-1.0631	1.3699	0.0064	-0.0498	-0.0737	0.0781	0.0443	0.3214	0.0947	-0.2485	-0.0507	0.108	-0.0149	0.0586	0.2139	0.0165	0.2548	-31.0913	137.2519	7.7133
50	0.9404	-0.141	0.3105	2.9656	-0.6938	0.7337	-0.0056	-0.2362	-0.0653	0.2995	0.0324	0.3149	0.0028	-0.1151	-0.0268	0.1276	0.0327	0.0904	0.1941	0.0051	0.1824	-24.5177	147.0187	17.8695
51	3.8035	1.762	-1.1751	6.9995	-2.3257	2.1081	0.0672	0.1374	0.2739	-0.247	-0.1156	-0.1362	-0.0317	0.2454	0.0485	0.0836	-0.0102	-0.021	0.2324	0.0224	0.2267	38.5783	155.6542	-0.6554
52	1.318	0.6581	-0.5369	0.812	0.0994	1.3584	-0.0395	-0.0624	-0.0442	0.0789	-0.0275	-0.1129	0.1456	0.1192	0.067	0.1578	0.0304	-0.0598	0.1881	0.0303	0.1696	31.5217	136.8767	17.513
53	2.3629	1.8563	-2.3819	3.4422	-4.7789	7.4583	-0.0901	0.0951	-0.0502	-0.1649	0.1281	-0.025	0.2902	-0.0897	-0.0381	0.1252	-0.0116	-0.0385	0.1526	0.0007	0.1869	27.1482	145.0057	7.5428
54	0.6816	-0.3302	0.4102	1.2443	-1.2175	2.3459	0.0036	-0.0418	-0.0247	0.0934	-0.0561	-0.2854	-0.0093	0.2913	0.0526	0.12	-0.0051	-0.0522	0.2243	0.0158	0.2248	40.0131	145.1754	6.3772
55	0.6224	-0.0834	-0.2292	0.575	-0.5869	2.0187	0.0174	-0.0694	0.0686	0.213	-0.0103	-0.1416	-0.1371	0.1633	-0.0071	0.1457	-0.038	-0.0636	0.1694	-0.0039	0.1953	31.1208	156.0995	12.6561
56	4.8386	-1.693	2.6583	3.0793	-2.1324	5.4433	-0.0004	0.4663	0.1991	-0.1808	0.0334	0.4116	-0.2307	-0.2461	-0.033	0.0998	-0.0335	-0.0645	0.2021	-0.0056	0.247	-30.2449	139.8054	-15.4106
57	2.2935	-0.9506	0.8323	2.1214	-0.1416	1.3154	-0.0196	-0.0882	-0.1574	0.1824	0.0355	0.1798	0.1094	0.0036	-0.0158	0.1402	-0.0593	0.0145	0.1421	0.0296	0.2295	-22.6133	122.1196	3.7109
58	1.8042	-1.6506	1.5033	8.8106	-5.5646	3.6565	-0.1182	-0.0253	0.008	0.0909	-0.0652	-0.1437	-0.0904	-0.0052	0.1834	0.1747	-0.02	-0.0251	0.2026	-0.0107	0.2139	-18.4138	131.4944	-4.3372
59	0.5006	-0.1458	-0.0705	0.8221	-0.1683	0.7819	-0.0147	0.0146	-0.138	0.0142	0.0961	0.3154	0.1408	-0.2819	-0.0813	0.0972	-0.065	-0.0454	0.1646	0.0024	0.2524	-29.3024	130.5899	-8.334
60	1.3533	-0.8412	0.1669	5.4868	-1.7997	1.3603	0.0142	0.1293	-0.1221	-0.3204	0.0033	0.0422	0.2426	-0.1065	-0.0175	0.1458	-0.0639	-0.0459	0.1892	-0.0485	0.1849	-19.7043	126.7677	-16.985

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	23 - 40
2	X-RAY DIFFRACTION	2	A	41 - 66
3	X-RAY DIFFRACTION	3	A	67 - 128
4	X-RAY DIFFRACTION	4	A	129 - 147
5	X-RAY DIFFRACTION	5	A	148 - 172
6	X-RAY DIFFRACTION	6	B	22 - 27
7	X-RAY DIFFRACTION	7	B	28 - 77
8	X-RAY DIFFRACTION	8	B	78 - 112
9	X-RAY DIFFRACTION	9	B	113 - 123
10	X-RAY DIFFRACTION	10	B	124 - 172
11	X-RAY DIFFRACTION	11	C	23 - 75
12	X-RAY DIFFRACTION	12	C	76 - 111
13	X-RAY DIFFRACTION	13	C	112 - 122
14	X-RAY DIFFRACTION	14	C	123 - 141
15	X-RAY DIFFRACTION	15	C	142 - 172
16	X-RAY DIFFRACTION	16	D	21 - 26
17	X-RAY DIFFRACTION	17	D	27 - 75
18	X-RAY DIFFRACTION	18	D	76 - 112
19	X-RAY DIFFRACTION	19	D	113 - 141
20	X-RAY DIFFRACTION	20	D	142 - 172
21	X-RAY DIFFRACTION	21	E	24 - 50
22	X-RAY DIFFRACTION	22	E	51 - 75
23	X-RAY DIFFRACTION	23	E	76 - 114
24	X-RAY DIFFRACTION	24	E	115 - 144
25	X-RAY DIFFRACTION	25	E	145 - 172
26	X-RAY DIFFRACTION	26	F	22 - 27
27	X-RAY DIFFRACTION	27	F	28 - 59
28	X-RAY DIFFRACTION	28	F	60 - 75
29	X-RAY DIFFRACTION	29	F	76 - 108
30	X-RAY DIFFRACTION	30	F	109 - 172
31	X-RAY DIFFRACTION	31	G	23 - 54
32	X-RAY DIFFRACTION	32	G	55 - 79
33	X-RAY DIFFRACTION	33	G	80 - 112
34	X-RAY DIFFRACTION	34	G	113 - 138
35	X-RAY DIFFRACTION	35	G	139 - 172
36	X-RAY DIFFRACTION	36	H	22 - 37
37	X-RAY DIFFRACTION	37	H	38 - 64
38	X-RAY DIFFRACTION	38	H	65 - 115
39	X-RAY DIFFRACTION	39	H	116 - 141
40	X-RAY DIFFRACTION	40	H	142 - 172
41	X-RAY DIFFRACTION	41	I	22 - 42
42	X-RAY DIFFRACTION	42	I	43 - 70
43	X-RAY DIFFRACTION	43	I	71 - 110
44	X-RAY DIFFRACTION	44	I	111 - 138
45	X-RAY DIFFRACTION	45	I	139 - 172
46	X-RAY DIFFRACTION	46	J	21 - 28
47	X-RAY DIFFRACTION	47	J	29 - 62
48	X-RAY DIFFRACTION	48	J	63 - 72
49	X-RAY DIFFRACTION	49	J	73 - 111
50	X-RAY DIFFRACTION	50	J	112 - 172
51	X-RAY DIFFRACTION	51	K	21 - 37
52	X-RAY DIFFRACTION	52	K	38 - 59
53	X-RAY DIFFRACTION	53	K	60 - 76
54	X-RAY DIFFRACTION	54	K	77 - 113
55	X-RAY DIFFRACTION	55	K	114 - 172
56	X-RAY DIFFRACTION	56	L	21 - 37
57	X-RAY DIFFRACTION	57	L	38 - 59
58	X-RAY DIFFRACTION	58	L	60 - 75
59	X-RAY DIFFRACTION	59	L	76 - 135
60	X-RAY DIFFRACTION	60	L	136 - 172

-
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

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 5 types, 829 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, 12 molecules ABCDEFGHIJKL

-Non-polymers , 5 types, 829 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, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 5 types, 829 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