PDB-2xkq: Crystal structure of Streptococcus suis Dpr with manganese

ID or keywords:

Entry

Database: PDB / ID: 2xkq

Title

Crystal structure of Streptococcus suis Dpr with manganese

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: 2.4 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 12, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 24, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 24, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4	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_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_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.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_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	2xkq.cif.gz	728.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2xkq.ent.gz	612.9 KB	Display	PDB format
PDBx/mmJSON format	2xkq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2xkq_validation.pdf.gz	519.9 KB	Display	wwPDB validaton report
Full document	2xkq_full_validation.pdf.gz	533.8 KB	Display
Data in XML	2xkq_validation.xml.gz	66.6 KB	Display
Data in CIF	2xkq_validation.cif.gz	92.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xk/2xkq ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xkq	HTTPS FTP

-
Related structure data

Related structure data	2xjmC 2xjnC 2xjoC 1umn 2bw1 2cf7 2ux1 2v15 C: citing same article (ref.)
Similar structure data	6hvq-1 2bkc-1 2iy4-2 2xjm-d 2xjo-d 6sev-1 2bk6-1 2iy4-1 6hv1-1 1qgh-d 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	#57 - Sep 2004 Catalase similarity (2) #35 - Nov 2002 Ferritin and Transferrin similarity (3) #114 - Jun 2009 Vaults 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)	106.222, 139.467, 143.827
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, 555 molecules

#2: Chemical	ChemComp-MN3 / MANGANESE (III) ION Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.3 Å³/Da / Density % sol: 45.8 % / Description: NONE
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: BW7A / Wavelength: 0.9
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2008 / Details: VERTICALLY FOCUSSING
Radiation	Monochromator: FIXED EXIT DOUBLE CRYSTAL SI (111), HORIZONTALLY FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 83975 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / B_iso Wilson estimate: 46.6 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 14.1
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.4.0078	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.4→49 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.921 / SU B: 19.274 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.261 / 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	0.2449	4190	5 %	RANDOM
R_work	0.183	-	-	-
obs	0.18611	79708	99.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 12.711 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	0 Å²	0 Å²
2-	-	-0.94 Å²	0 Å²
3-	-	-	1.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14494	0	82	529	15105

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	14881
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.333	1.951	20119
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.017	5	1800
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	44.728	25.168	745
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.947	15	2618
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.963	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	2193
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11260
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	0.48	1.5	9000
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.945	2	14434
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.78	3	5881
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.818	4.5	5685
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: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	320	-
R_work	0.236	5796	-
obs	-	-	99.82 %

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	4.1535	3.7166	-0.1119	10.5738	8.2526	9.6287	-0.3256	0.4417	-0.346	-0.2875	0.2161	-0.2057	0.4962	0.6359	0.1095	0.4484	0.069	-0.0383	0.3145	0.0462	0.4332	16.418	100.419	13.954
2	0.1187	0.5622	0.2027	3.1208	1.6977	1.5338	-0.0229	-0.1231	-0.1608	0.292	-0.0266	0.0034	0.1184	0.1069	0.0495	0.3533	0.0607	-0.0666	0.2692	0.0969	0.3104	13.076	124.498	25.855
3	1.6402	0.4103	0.0564	1.493	1.2668	2.3581	-0.06	-0.177	-0.3304	0.3196	-0.0688	-0.0442	0.1965	0.0376	0.1288	0.3887	0.0576	-0.0472	0.1419	0.137	0.375	10.915	112.689	25.312
4	1.9989	-1.1685	-0.5032	7.957	6.1905	6.7387	-0.0113	-0.1436	-0.506	0.69	-0.0411	-0.0343	0.8455	0.1595	0.0524	0.3202	0.0985	-0.0849	0.2428	0.118	0.4159	22.942	113.251	20.968
5	0.9547	1.7162	0.4019	4.1685	0.8343	0.1807	-0.1979	-0.0008	-0.2846	-0.0791	0.0856	-0.2089	-0.0651	0.2088	0.1123	0.325	0.1036	-0.086	0.2798	0.0727	0.3884	25.602	121.121	17.962
6	0.541	-2.2214	0.18	26.8981	8.4928	4.8542	0.0901	0.3716	0.1348	-0.7032	-0.3093	0.6532	-0.7909	-0.2558	0.2192	0.4296	0.0102	-0.0106	0.5045	0.0429	0.3306	-6.184	151.999	-38.502
7	0.717	-0.4442	-0.9873	1.6661	0.5503	1.3623	0.0025	0.1109	0.1124	-0.1436	0.0148	0.0372	-0.2154	0.0325	-0.0173	0.1753	-0.0082	-0.0085	0.3332	0.0734	0.311	-5	164.35	-14.222
8	4.22	-3.2424	-4.7844	3.9668	4.8477	9.5234	0.0625	0.0242	-0.1138	-0.0006	0.0368	-0.1465	0.1055	0.2388	-0.0993	0.2729	-0.024	-0.0387	0.3467	0.0168	0.304	-3.04	154.345	-16.789
9	1.2713	-0.4199	-0.075	1.0169	0.3017	0.4763	-0.0092	0.3588	0.2452	-0.2461	0.0054	0.0969	-0.1311	-0.027	0.0038	0.2252	0.0052	-0.0113	0.3569	0.0959	0.2447	-4.858	163.7	-23.597
10	2.6954	-1.537	-2.0096	2.6767	1.369	2.2174	0.0435	0.3467	-0.1714	-0.3524	-0.0833	0.3349	-0.0222	-0.2032	0.0398	0.2019	-0.0045	-0.107	0.3376	0.0279	0.3005	-15.181	152.544	-23.152
11	1.2244	0.0694	0.5124	1.1132	0.4462	1.5576	0.0849	-0.0506	-0.2627	0.273	0.1433	0.1252	0.1023	-0.0216	-0.2282	0.3464	0.0262	0.0434	0.2116	0.1201	0.3563	-3.659	117.865	20.48
12	1.113	0.1093	0.3674	2.5262	1.871	2.6925	-0.0055	-0.289	-0.3271	0.4605	0.1	0.1346	0.3137	-0.0292	-0.0945	0.4382	0.0503	0.0077	0.149	0.204	0.2881	-0.852	116.205	30.524
13	7.587	-0.5022	0.1231	7.8413	5.2093	8.7724	0.0335	0.0697	-0.8195	0.2919	0.2486	0.1421	0.2308	-0.1049	-0.2821	0.3778	-0.025	0.0296	0.1857	0.1178	0.4052	-12.626	109.549	18.068
14	0.5536	0.0268	0.6643	8.3855	4.3799	4.2104	0.3752	-0.6045	-0.2757	0.9998	0.0177	-0.1663	0.0847	-0.7691	-0.3929	0.4783	0.045	0.1799	0.3762	0.1738	0.2586	-13.807	125.592	33.461
15	2.5816	1.6594	2.3176	1.168	1.1738	3.0659	-0.0595	-0.2134	-0.0544	0.1826	0.02	0.5027	0.0295	-0.1965	0.0395	0.3194	0.0131	0.113	0.2729	0.1372	0.3815	-16.207	124.072	21.544
16	4.5148	3.1228	4.4459	11.3426	7.055	6.103	-0.2391	-0.5212	0.4931	0.5832	-0.1676	0.2152	-0.5767	-0.0241	0.4067	0.4152	-0.0034	-0.0007	0.33	0.0463	0.3855	13.172	182.064	-7.008
17	0.2242	-0.6541	-0.4911	2.1374	1.0714	1.648	0.0671	0.2844	0.0849	-0.2524	-0.1128	-0.1653	0.0533	-0.0656	0.0457	0.1975	-0.0212	0.0296	0.3831	0.0541	0.2828	13.156	156.096	-21.249
18	0.6523	-0.5818	-0.3639	2.0537	1.2127	2.3379	0.047	0.2253	0.2417	-0.2369	-0.0132	-0.2038	-0.1527	-0.0023	-0.0337	0.1519	-0.0431	0.0446	0.3276	0.0955	0.317	9.929	166.952	-19.828
19	2.183	-1.2888	-1.5724	5.2865	3.5123	3.7416	0.0879	0.1372	0.4519	-0.3542	-0.0035	-0.478	-0.3384	0.1217	-0.0844	0.1675	-0.0565	0.0334	0.327	0.1301	0.3306	21.53	167.856	-15.448
20	2.6581	-2.4156	-1.6531	3.7534	1.473	1.0286	-0.0083	0.1522	0.1482	0.0103	-0.073	-0.2117	0.0055	-0.0197	0.0814	0.1569	-0.0384	0.0252	0.3824	0.0837	0.3326	24.716	160.205	-12.191
21	16.4578	-1.2557	-0.6161	1.3439	1.7304	2.2935	0.2307	0.2821	-1.2297	0.4756	0.0557	0.2932	0.6517	0.0783	-0.2863	0.523	0.054	0.0163	0.3458	-0.0693	0.5238	25.822	105.834	-15.558
22	5.53	-0.3474	-0.3306	0.5144	-0.263	0.5324	-0.0143	0.2964	-0.1979	-0.2254	0.0571	0.0443	0.3529	-0.0476	-0.0428	0.3692	0.0367	-0.0284	0.152	-0.0857	0.3747	1.949	113.998	-11.274
23	1.8891	-0.924	0.3756	0.452	-0.1904	1.1398	0.0842	0.4457	-0.6286	-0.2945	-0.0707	0.0727	0.4255	0.1507	-0.0135	0.3997	0.056	-0.0039	0.1629	-0.2488	0.4118	8.594	109.458	-18.492
24	9.6684	1.3675	0.138	1.485	0.4398	2.1516	-0.3208	0.3433	-0.9083	-0.1448	0.1699	-0.1701	0.3921	0.306	0.1509	0.4128	0.1	-0.0132	0.095	-0.1309	0.5129	13.158	104.662	-7.459
25	6.8885	1.1593	-4.2344	1.8184	-0.9399	2.6348	0.1779	-0.3554	-0.6941	-0.0196	-0.1194	-0.1432	0.1062	0.1774	-0.0585	0.4069	0.0342	-0.0467	0.181	-0.0532	0.458	9.175	107.897	-0.035
26	9.637	0.7266	0.0724	1.555	0.9661	1.5367	0.2543	-0.4094	0.3884	0.1526	-0.1474	-0.3886	-0.0517	0.0775	-0.1068	0.3794	0.0032	-0.0822	0.2358	-0.0655	0.3705	16.344	171.891	20.978
27	0.1109	-0.3512	0.0986	2.4715	0.6581	0.7801	-0.025	-0.1315	0.0419	0.2826	0.0745	0.1413	0.0269	-0.0809	-0.0495	0.2652	0.0466	0.0878	0.2614	-0.0048	0.315	-9.01	165.255	15.212
28	9.6262	0.1756	2.9698	0.3999	0.2393	1.2565	-0.0664	-0.255	-0.1737	0.1069	-0.0003	-0.041	0.0869	-0.0341	0.0667	0.3257	-0.002	0.0061	0.276	0.0056	0.3117	4.746	162.226	13.323
29	3.818	-0.0103	-0.2362	1.2695	-0.2322	0.537	0.0267	-0.3551	0.4036	0.4707	-0.0153	-0.0154	-0.2764	0.0178	-0.0114	0.392	0.0345	-0.0292	0.212	-0.0542	0.2525	4.741	170.189	23.384
30	2.9749	-0.6694	0.7937	0.8631	-0.5224	1.0601	-0.1534	0.0809	0.2893	0.2193	0.0573	-0.0711	-0.189	0.1129	0.0961	0.2494	-0.0033	-0.0103	0.2105	-0.006	0.3801	7.83	173.629	8.435
31	15.6117	1.759	1.5847	8.6019	3.0681	1.1544	0.191	0.6515	-0.5248	-0.4905	-0.2163	0.7856	-0.2912	-0.5155	0.0254	0.4487	0.0062	-0.0429	0.4329	-0.0553	0.4137	-12.79	120.356	-32.342
32	4.8714	1.6118	0.5352	0.8145	0.0929	0.7709	0.0494	0.2788	-0.2055	-0.2332	-0.0202	-0.1115	0.2368	0.147	-0.0292	0.3663	0.0621	0.0335	0.3104	-0.1533	0.2431	12.227	126.188	-23.413
33	3.6473	0.3384	-0.2147	0.9732	-0.423	0.4993	0.0234	0.263	-0.1733	-0.3805	0.046	0.07	0.3836	0.0996	-0.0694	0.4286	0.0214	-0.034	0.3024	-0.1975	0.2218	3.549	120.437	-26.546
34	9.0096	2.2488	-1.0844	0.9649	-0.2432	1.017	-0.0261	0.6914	-0.3209	-0.3627	0.005	0.0882	0.1629	-0.0904	0.0211	0.4074	0.0044	-0.0318	0.3773	-0.0915	0.2414	-1.223	129.337	-33.752
35	5.7704	2.9914	-1.1673	2.1758	-1.1459	0.7041	-0.0126	0.5196	-0.0595	-0.2815	0.1019	0.2013	0.1108	-0.008	-0.0892	0.3548	0.0143	-0.0232	0.4537	-0.1196	0.2068	0.384	136.032	-29.89
36	6.437	-0.4199	0.194	3.6406	-0.2152	1.5497	-0.1419	-0.2808	0.2169	0.3166	0.0582	0.2282	-0.0302	-0.1815	0.0837	0.4663	0.0998	0.0949	0.3463	-0.0369	0.1755	-8.331	158.119	32.594
37	1.7358	-1.1902	0.039	1.6942	-0.2764	0.3994	-0.0174	-0.1926	0.1058	0.2496	0.0315	-0.2173	-0.0516	0.1235	-0.0141	0.4084	0.014	-0.069	0.2919	-0.0066	0.252	14.967	152.208	27.462
38	4.4353	-0.3891	0.8369	1.3441	-0.2629	0.7011	-0.0845	-0.1542	0.1995	0.5472	0.0532	0.0228	-0.1364	0.0266	0.0313	0.4856	0.0443	0.0387	0.2593	-0.0371	0.1743	-0.023	159.057	30.411
39	10.8913	1.2937	-3.5915	1.4202	-2.1594	3.5549	0.1809	-0.6039	0.4787	0.2975	-0.1267	-0.0194	-0.3273	0.0559	-0.0541	0.4511	0.0405	-0.0167	0.2958	-0.0293	0.2609	8.092	150.251	37.468
40	6.2756	-2.2849	1.7361	2.2716	-0.7702	0.8313	0.0324	-0.3798	-0.1609	0.5548	0.0654	0.2197	-0.1185	-0.1604	-0.0979	0.5398	0.0312	0.1221	0.3029	0.0501	0.1259	-4.398	145.002	35.252
41	0.9118	-1.6801	-0.544	15.7072	-0.263	0.4515	-0.4243	0.3132	-0.5105	0.3207	-0.101	-0.7838	0.6064	0.3148	0.5254	0.3822	0.0993	0.0143	0.3979	0.0374	0.4725	41.474	119.919	9.723
42	0.4361	0.2805	-0.5851	1.6409	-1.2957	2.1585	-0.0297	0.1172	-0.0028	-0.0591	-0.0561	-0.2053	0.0919	0.2438	0.0858	0.1864	0.0485	0.0459	0.3063	-0.0304	0.3713	32.831	139.286	-7.586
43	1.0159	0.373	0.1504	2.1025	-1.5586	3.391	0.0132	0.1239	-0.0604	0.1077	-0.1213	-0.4504	0.1568	0.374	0.1081	0.0883	0.1131	0.0015	0.2994	-0.0015	0.43	38.907	134.584	0.557
44	3.286	0.1282	-0.4959	2.7418	-3.5202	6.6895	-0.0639	0.0503	-0.4256	-0.1413	-0.0315	-0.3816	0.6798	0.4218	0.0954	0.2635	0.1396	0.0315	0.222	-0.0609	0.4168	34.309	122.079	-2.766
45	0.4554	1.9028	0.9155	7.9496	3.8247	1.8401	0.0198	0.2905	-0.272	-0.3692	-0.1907	-0.4158	0.2819	0.3289	0.1709	0.2777	0.1267	0.1043	0.4348	-0.0907	0.3895	30.817	126.467	-19.138
46	9.0458	-1.0946	12.2688	9.1705	-1.4846	16.6403	-0.2547	-1.1824	-0.6102	0.1348	-0.0313	0.8578	1.7138	-1.2295	0.2859	0.434	-0.0547	0.2447	0.5487	0.2017	0.5552	-31.775	129.631	25.017
47	0.8724	0.224	-0.1362	1.2522	-1.1453	1.8053	-0.1236	-0.0272	0.0153	-0.0537	0.1561	0.2862	0.122	-0.0799	-0.0325	0.1576	0.0321	0.0471	0.2827	0.0343	0.4115	-25.365	148.975	3.335
48	1.7773	1.7176	-0.7764	9.8579	-4.1237	2.2616	-0.0206	0.0064	-0.1293	-0.1089	0.0308	-0.0689	0.2169	0.1648	-0.0102	0.2679	0.009	0.0405	0.3496	0.0023	0.3327	-19.883	142.144	8.562
49	0.6332	-0.0537	-0.306	3.888	-1.28	2.0071	0.0288	-0.0233	-0.0483	0.1596	0.0425	0.6177	0.082	-0.3362	-0.0713	0.0714	0.0061	0.0756	0.3134	0.0486	0.4325	-32.054	141.587	7.337
50	0.8725	-0.4488	0.2541	3.9299	-0.6125	0.4143	-0.0009	-0.2945	0.0037	0.4497	0.0291	0.5338	-0.0552	-0.0273	-0.0282	0.2122	0.0598	0.1459	0.3148	0.0302	0.3633	-24.676	148.709	18.547
51	1.3048	0.8949	-0.7281	1.7778	-0.2314	0.7389	-0.0994	0.0082	0.016	-0.0574	0.0786	-0.2985	0.1877	0.1959	0.0208	0.1828	0.0446	-0.1061	0.3285	0.0415	0.3641	34.074	145.737	11.172
52	2.0354	1.8017	-3.3138	4.908	-4.8801	10.9397	-0.0876	0.1618	-0.0912	-0.1644	-0.0074	-0.0277	0.2948	-0.2124	0.0949	0.221	-0.0151	-0.0367	0.2835	-0.0101	0.3512	28.226	148.236	5.846
53	1.3028	-0.2847	0.7275	2.7927	-2.4919	5.0359	0.0605	0.0319	-0.0318	0.0884	-0.1475	-0.5589	-0.0997	0.5083	0.087	0.0583	0.0159	-0.0832	0.306	0.017	0.3992	40.686	147.324	5.729
54	0.8818	0.3718	-0.9451	3.9541	-3.9127	4.9962	0.0941	-0.1492	0.2256	0.2547	-0.003	-0.3769	-0.159	0.4696	-0.0911	0.1728	-0.0681	-0.1542	0.3039	-0.0104	0.4017	35.563	158.472	11.091
55	1.4023	0.4761	-1.3725	0.2177	-0.9424	5.3927	0.093	-0.0754	0.1254	0.2678	0.1596	-0.0776	-0.2221	0.1734	-0.2525	0.267	-0.0272	-0.1091	0.2399	-0.0218	0.356	27.812	157.902	15.094
56	1.7164	-0.1722	0.2323	1.1544	-0.8586	2.3127	-0.0261	0.0356	-0.1952	0.108	0.0512	0.4004	-0.0059	-0.1468	-0.0251	0.1774	-0.0839	-0.0237	0.2251	-0.0067	0.434	-25.219	130.043	-2.828
57	1.1891	-2.5896	1.8118	10.3218	-6.1596	4.6461	-0.103	-0.0163	0.0893	0.2495	-0.042	-0.0415	-0.2217	0.0722	0.145	0.2703	-0.0224	-0.0195	0.3309	-0.0043	0.3306	-19.245	134.648	-4.914
58	0.6346	0.0742	0.0637	3.2054	-0.8665	1.9425	-0.0824	0.0393	-0.1025	-0.0112	0.1486	0.5216	0.0281	-0.4329	-0.0662	0.0767	-0.0524	-0.0143	0.2831	0.0333	0.4469	-32.241	137.165	-5.254
59	1.0812	0.4638	-0.914	9.1926	-6.2573	5.9173	0.1375	0.2329	-0.1329	-0.4741	-0.0406	0.406	0.2899	-0.1615	-0.0969	0.1928	-0.0837	-0.1055	0.293	-0.067	0.3994	-25.603	131.206	-15.909
60	1.3379	-0.6982	-0.1144	7.6474	-1.8895	0.5315	0.0062	0.1953	-0.2287	-0.4512	0.0868	0.3509	0.2162	-0.2149	-0.0931	0.2916	-0.1082	-0.103	0.2671	-0.0626	0.4151	-18.932	122.826	-14.039

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	22 - 28
2	X-RAY DIFFRACTION	2	A	29 - 72
3	X-RAY DIFFRACTION	3	A	73 - 112
4	X-RAY DIFFRACTION	4	A	113 - 141
5	X-RAY DIFFRACTION	5	A	142 - 172
6	X-RAY DIFFRACTION	6	B	22 - 27
7	X-RAY DIFFRACTION	7	B	28 - 62
8	X-RAY DIFFRACTION	8	B	63 - 75
9	X-RAY DIFFRACTION	9	B	76 - 123
10	X-RAY DIFFRACTION	10	B	124 - 172
11	X-RAY DIFFRACTION	11	C	24 - 75
12	X-RAY DIFFRACTION	12	C	76 - 111
13	X-RAY DIFFRACTION	13	C	112 - 120
14	X-RAY DIFFRACTION	14	C	121 - 141
15	X-RAY DIFFRACTION	15	C	142 - 172
16	X-RAY DIFFRACTION	16	D	21 - 26
17	X-RAY DIFFRACTION	17	D	27 - 69
18	X-RAY DIFFRACTION	18	D	70 - 112
19	X-RAY DIFFRACTION	19	D	113 - 141
20	X-RAY DIFFRACTION	20	D	142 - 172
21	X-RAY DIFFRACTION	21	E	22 - 27
22	X-RAY DIFFRACTION	22	E	28 - 75
23	X-RAY DIFFRACTION	23	E	76 - 113
24	X-RAY DIFFRACTION	24	E	114 - 141
25	X-RAY DIFFRACTION	25	E	142 - 172
26	X-RAY DIFFRACTION	26	F	22 - 37
27	X-RAY DIFFRACTION	27	F	38 - 59
28	X-RAY DIFFRACTION	28	F	60 - 76
29	X-RAY DIFFRACTION	29	F	77 - 112
30	X-RAY DIFFRACTION	30	F	113 - 172
31	X-RAY DIFFRACTION	31	G	22 - 28
32	X-RAY DIFFRACTION	32	G	29 - 67
33	X-RAY DIFFRACTION	33	G	68 - 115
34	X-RAY DIFFRACTION	34	G	116 - 138
35	X-RAY DIFFRACTION	35	G	139 - 172
36	X-RAY DIFFRACTION	36	H	22 - 40
37	X-RAY DIFFRACTION	37	H	41 - 65
38	X-RAY DIFFRACTION	38	H	66 - 113
39	X-RAY DIFFRACTION	39	H	114 - 123
40	X-RAY DIFFRACTION	40	H	124 - 172
41	X-RAY DIFFRACTION	41	I	23 - 28
42	X-RAY DIFFRACTION	42	I	29 - 67
43	X-RAY DIFFRACTION	43	I	68 - 114
44	X-RAY DIFFRACTION	44	I	115 - 159
45	X-RAY DIFFRACTION	45	I	160 - 172
46	X-RAY DIFFRACTION	46	J	21 - 26
47	X-RAY DIFFRACTION	47	J	27 - 62
48	X-RAY DIFFRACTION	48	J	63 - 75
49	X-RAY DIFFRACTION	49	J	76 - 113
50	X-RAY DIFFRACTION	50	J	114 - 172
51	X-RAY DIFFRACTION	51	K	21 - 62
52	X-RAY DIFFRACTION	52	K	63 - 76
53	X-RAY DIFFRACTION	53	K	77 - 112
54	X-RAY DIFFRACTION	54	K	113 - 141
55	X-RAY DIFFRACTION	55	K	142 - 172
56	X-RAY DIFFRACTION	56	L	22 - 61
57	X-RAY DIFFRACTION	57	L	62 - 75
58	X-RAY DIFFRACTION	58	L	76 - 110
59	X-RAY DIFFRACTION	59	L	111 - 147
60	X-RAY DIFFRACTION	60	L	148 - 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://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, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 5 types, 555 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, 555 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, 555 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