PDB-2pli: Crystal structure of putative Mg2+ and Co2+ transporter(CorC)asso...

ID or keywords:

Entry

Database: PDB / ID: 2pli

Title

Crystal structure of putative Mg2+ and Co2+ transporter(CorC)associated region from Neisseria meningitidis MC58

Components

Uncharacterized protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / CorC-associated region / MCSG / PSI2 / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

flavin adenine dinucleotide binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Neisseria meningitidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Nocek, B. / Duggan, E. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Structure of putative Mg2+ and Co2+ transporter(CorC)associated region from Neisseria meningitidis MC58.
Authors: Nocek, B. / Duggan, E. / Gu, M. / Joachimiak, A.

History

Deposition	Apr 19, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2pli.cif.gz	100.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2pli.ent.gz	77.5 KB	Display	PDB format
PDBx/mmJSON format	2pli.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pl/2pli ftp://data.pdbj.org/pub/pdb/validation_reports/pl/2pli	HTTPS FTP

-
Related structure data

Similar structure data	2re3-d 2emt-1 3glk-d 3dxb-2 3c3s-4 6x1g-1 6itq-d 6gy4-d 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	TargetDB: APC83979.1

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (2) #140 - Aug 2011 Rhomboid Protease GlpG similarity (3)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

B: Uncharacterized protein

C: Uncharacterized protein

hetero molecules

A: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.718, 67.991, 129.044
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Uncharacterized protein Mass: 10123.986 Da / Num. of mol.: 4 / Fragment: Residues 187-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0537 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9K0P8
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Zinc acetate, 0.1M Imidazole, 10% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	19-ID	1	0.9794
SYNCHROTRON	APS	19-BM	2	1.282

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 315	1	CCD	Mar 19, 2007	mirrors
SBC-3	2	CCD	Apr 1, 2007

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	1.282	1

Reflection

Resolution: 1.7→30 Å / Num. all: 52593 / Num. obs: 52593 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / R_merge(I) obs: 0.075 / Net I/σ(I): 25.1

Reflection shell

Resolution: 1.7→1.73 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 2.83 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.7→30 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.938 / SU B: 2.852 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21539	2677	5.1 %	RANDOM
R_work	0.17663	-	-	-
all	0.1798	52593	-	-
obs	0.17854	49805	99.59 %	-

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: 10.282 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.37 Å²	0 Å²	0 Å²
2-	-	0.24 Å²	0 Å²
3-	-	-	0.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2569	0	49	455	3073

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	2776
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1850
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.935	3764
X-RAY DIFFRACTION	r_angle_other_deg	0.932	3	4471
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.023	5	353
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.552	22.937	143
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.186	15	466
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.932	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	425
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3192
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	604
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	539
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	2047
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	1355
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	1610
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	322
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.225	0.2	18
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.378	0.2	44
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.475	0.2	45
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.265	0.2	27
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.348	0.2	5
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.277	1.5	2053
X-RAY DIFFRACTION	r_mcbond_other	0.272	1.5	707
X-RAY DIFFRACTION	r_mcangle_it	1.598	2	2751
X-RAY DIFFRACTION	r_scbond_it	3.092	3	1141
X-RAY DIFFRACTION	r_scangle_it	4.355	4.5	1010
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.745 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.276	196	-
R_work	0.205	3591	-
obs	-	-	98.98 %

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	7.713	-1.1429	-6.9064	4.2585	0.4782	15.2208	0.0566	0.001	-0.2259	-0.0421	-0.1584	0.3234	-0.2508	-0.4226	0.1017	-0.0137	-0.0006	-0.0584	0.0545	0.0042	0.0519	24.3896	5.0292	13.2665
2	6.7381	-0.0027	5.1352	0.3218	-0.9345	6.6151	-0.049	0.3433	0.0465	0.0042	-0.0866	0.1171	-0.1846	0.2686	0.1356	0.0531	-0.0044	-0.0429	0.0425	0.0327	0.0202	29.4824	9.4743	4.1852
3	1.7766	-0.1467	0.8353	2.0379	-3.8313	17.4204	-0.059	-0.131	0.0262	0.1276	0.0498	0.1188	-0.2989	-0.1303	0.0092	0.0391	-0.0054	-0.0182	0.0322	0.005	0.0317	30.1062	5.8796	13.4967
4	1.4443	0.149	0.6833	2.0826	-0.1094	2.5682	0.0558	-0.0304	-0.2145	-0.0959	-0.0211	-0.0971	0.0793	0.0716	-0.0347	0.0256	0.0049	-0.0201	0.0023	0.0156	0.0725	32.0992	-4.6885	11.4682
5	7.7298	-5.0416	3.5877	5.2549	-0.605	5.3329	0.1422	-0.4626	-0.5365	0.3169	-0.1702	-0.9438	0.048	0.3618	0.0281	-0.04	-0.0385	-0.127	0.0086	0.1076	0.2694	41.2152	-8.6436	16.587
6	9.7928	3.1723	1.0424	1.1572	0.3661	0.7537	0.2323	-0.1405	-0.4727	-0.0255	-0.0301	-0.1965	0.1116	0.0678	-0.2023	-0.0071	0.014	-0.0302	0.0375	0.0311	0.0885	42.3774	-0.4786	18.4738
7	1.4446	-1.679	0.6332	2.7098	-1.4556	3.2844	-0.0154	-0.0384	0.0098	0.0353	-0.1272	0.0273	-0.2467	0.1443	0.1426	0.0173	-0.0203	-0.0042	0.0587	0.0204	0.0438	42.8635	11.3675	17.991
8	13.8851	-0.9116	3.5048	4.7688	0.8661	9.2596	0.0735	0.3653	-0.3918	-0.2925	-0.0828	-0.4624	0.0481	0.1611	0.0094	-0.0099	0.0206	0.0371	0.0258	-0.0104	0.0578	42.1678	2.3739	7.6769
9	1.785	-0.6575	-0.5277	0.3918	0.601	9.6299	0.0722	-0.203	0.0917	0.032	0.0038	-0.0085	-0.1077	0.0864	-0.076	0.0288	-0.0355	-0.0138	0.0603	-0.0099	0.0184	38.3723	8.825	23.7698
10	1.2533	0.987	2.5176	0.8632	1.6513	6.3365	-0.0754	0.1325	0.0382	-0.062	0.0898	-0.0162	0.0822	0.5609	-0.0143	0.0353	0.0096	-0.0119	0.0732	0.0179	0.022	37.0872	5.9064	8.6895
11	4.0105	2.2449	-1.2604	6.6616	-4.313	2.8039	-0.2428	-0.2442	0.1528	0.0906	0.1705	-0.2497	0.0217	0.1373	0.0723	0.042	0.0398	0.0091	0.0458	-0.0162	0.0299	20.1438	-5.4204	22.9102
12	0.6224	0.1006	-0.4517	26.1849	-5.3947	2.0615	-0.1551	-0.2483	0.0544	0.1612	0.2655	0.4789	0.0032	0.1008	-0.1104	-0.0071	0.0408	-0.0146	0.0778	0.0341	0.0246	14.6181	-8.3914	24.7557
13	1.9132	-0.1216	0.5654	2.2915	-0.3697	1.1484	-0.0435	0.0245	0.0308	-0.1425	0.058	0.0978	0.0975	0.0083	-0.0145	0.0154	0.006	-0.0225	0.0494	0.0285	0.0427	12.9169	-3.1224	13.7779
14	2.6653	-1.2468	0.7603	32.872	-13.2064	5.3314	0.1883	0.177	-0.2709	-0.7528	0.1796	1.0515	-0.0475	-0.5039	-0.3679	-0.0036	0.0299	-0.067	0.0999	0.0481	0.0522	4.5756	-1.1939	9.821
15	6.535	0.1588	-2.7197	1.567	2.5581	5.5374	0.0346	0.1199	0.4603	-0.1671	0.0271	0.1192	-0.1511	-0.27	-0.0618	-0.0121	0.0276	-0.0388	0.054	0.0307	0.0914	7.8455	5.6486	15.0169
16	14.4774	-2.9313	-1.2366	4.5409	2.5919	2.4317	-0.2077	-0.0922	0.0801	-0.062	0.1819	0.1122	0.0476	0.0174	0.0258	-0.0521	0.0189	-0.0299	0.0851	0.0089	0.0555	1.2962	5.0322	20.8277
17	5.1895	-1.3897	1.9525	7.6355	-1.3314	5.3648	-0.242	-0.8467	0.0924	0.2178	0.0834	0.3294	0.0394	-0.1555	0.1586	-0.0758	0.0396	0.0194	0.1527	-0.0144	0.0434	3.8643	4.0513	29.8748
18	3.9628	2.5661	1.6966	4.9192	3.0107	2.8648	0.0394	-0.0611	-0.2036	0.2106	-0.0695	0.2177	0.0024	-0.1882	0.0301	-0.072	-0.0005	-0.0186	0.0756	0.0429	0.0862	5.6134	-3.8508	23.7831
19	9.0484	-7.582	7.2294	31.6284	-5.2821	11.7167	-0.2763	-0.3187	0.9713	-0.2008	-0.2966	0.0849	-0.5523	0.5063	0.5729	0.0106	0.023	-0.0711	0.0503	-0.0981	0.0788	11.4157	12.4978	28.9962
20	0.9368	0.1641	-0.143	13.2683	0.8923	0.0854	-0.1072	-0.2774	-0.1779	-0.1423	0.0422	0.2058	-0.1107	-0.0851	0.065	-0.0248	-0.0048	-0.0065	0.0841	0.0433	0.0561	9.9444	-3.4748	24.9146
21	5.0399	-6.686	2.9267	13.6777	-6.4185	3.9422	-0.0043	-0.1348	-0.0288	0.2509	0.0198	0.0022	-0.2231	0.0233	-0.0155	0.0345	-0.0186	-0.0323	0.0243	0.032	0.0378	19.5763	4.6421	6.2715
22	8.063	-2.317	0.0887	0.7243	0.6816	8.5561	-0.0853	0.2152	-0.123	-0.0833	0.0458	0.0745	0.0474	0.1777	0.0395	0.0535	-0.0054	-0.0419	0.0209	0.0141	0.0286	24.5846	0.66	0.9647
23	2.1354	0.1213	0.1433	4.2405	-3.4156	2.7784	0.0453	-0.0037	0.1451	0.2921	0.0405	0.0734	-0.1698	-0.0411	-0.0858	0.0644	-0.0007	-0.0091	0.0282	0.0189	0.0156	14.7011	11.9303	0.6802
24	3.2085	-2.9153	2.1544	2.6511	-2.0286	3.7323	0.1048	0.181	0.1459	-0.0162	-0.1355	-0.1189	0.016	0.1233	0.0308	0.0425	-0.0014	-0.0301	0.0203	0.0427	0.0351	18.5491	14.6176	-6.5198
25	1.5415	0.1754	3.3315	7.1394	0.7394	7.2183	0.2508	-0.1316	-0.0266	-0.3483	-0.0857	0.254	0.099	-0.0053	-0.1651	0.0764	0.0107	-0.0469	0.0109	0.027	0.0145	9.9865	10.2114	-8.3969
26	0.1091	0.4284	-1.0402	7.9045	-2.5413	10.3019	0.1935	-0.2511	-0.5161	-0.9143	0.1447	0.8044	0.4572	-0.5547	-0.3383	0.1831	-0.0853	-0.2737	-0.0538	0.0449	0.103	5.4367	1.6559	-10.9253
27	15.0668	6.5897	-8.2659	12.709	-5.4167	4.865	0.5814	-0.0709	-0.7644	-0.0109	-0.1975	-0.3691	0.2917	0.5234	-0.3839	0.1049	-0.0904	-0.137	0.021	0.0064	-0.0187	11.7971	-2.8321	-7.8406
28	13.5535	1.5051	0.7214	7.2414	-4.6083	14.4417	0.1424	0.3995	-0.1113	-0.1547	-0.0058	-0.108	0.1114	0.1221	-0.1366	0.0673	0.0208	-0.0375	0.0007	0.0125	-0.0304	19.4808	4.5721	-9.7015
29	26.6729	-4.538	-2.0752	4.3844	1.2763	5.6798	0.1533	-0.108	-0.3146	-0.2299	0.0083	0.6814	0.6461	-0.6551	-0.1615	0.0007	-0.1577	-0.1242	0.0375	0.0811	0.1119	3.3684	0.7604	-1.9061
30	6.1905	-1.4692	2.0248	1.2276	0.4173	1.5793	0.0047	0.2782	0.2203	-0.117	0.0989	0.0018	0.5305	-0.0311	-0.1036	0.0761	-0.0031	-0.0512	0.0058	0.0252	-0.0018	17.3005	2.82	-3.1277
31	11.0608	-1.5777	8.9738	4.0594	-2.3239	7.5647	-0.0502	0.0817	0.0589	0.1645	-0.0024	-0.2465	-0.1153	-0.0642	0.0526	0.0435	0.0242	-0.0031	0.0417	0.0038	0.0128	24.5336	-11.1151	20.724
32	11.7763	-4.8227	4.7604	10.4677	-1.2997	2.9485	0.103	-0.0319	-0.4301	-0.3417	0.108	0.142	0.0812	-0.2608	-0.211	0.0525	0.0037	-0.0083	0.0246	0.0337	0.0247	18.6772	-15.885	17.1059
33	2.1575	-0.3252	-0.375	5.9693	-3.4694	2.1651	-0.2044	-0.1583	0.0881	0.3188	-0.0885	-0.6539	-0.319	-0.0934	0.2929	0.0306	0.0104	-0.0731	0.0114	0.0061	0.0723	29.4471	-17.164	26.6144
34	2.1124	-1.1106	0.2726	4.6274	-2.7652	2.2763	-0.1439	-0.067	-0.0038	0.1414	0.1558	-0.0165	-0.0171	-0.282	-0.0119	0.0384	0.0495	-0.0123	0.0739	0.0191	-0.0079	21.8146	-22.3923	29.4426
35	10.0676	3.6718	4.6062	14.9331	-6.986	7.6319	0.0343	-0.4679	0.0035	-0.2932	-0.1512	-0.176	0.0871	-0.1864	0.1169	0.0123	0.0325	-0.0454	0.0579	0.0292	0.0195	33.0398	-27.5429	32.2992
36	1.1905	-3.3037	0.3923	14.4874	0.627	5.4144	-0.0051	-0.0577	0.231	-0.0309	-0.2672	-0.3291	0.4671	0.1119	0.2723	0.0579	0.0273	0.0092	-0.0054	0.0331	0.0467	32.4105	-28.2347	24.0615
37	5.4289	-3.7338	-8.0689	3.697	4.4556	13.0527	0.1715	0.3637	0.0141	0.3181	0.2362	-0.3904	-0.2369	-0.0575	-0.4076	0.0283	0.0755	0.059	-0.0166	0.0187	0.044	36.0755	-29.8994	16.5832
38	9.817	1.2971	-4.257	4.7215	-2.9774	3.3025	-0.2024	0.0891	-0.0957	-0.615	0.0842	-0.103	0.4502	-0.3025	0.1182	0.0994	0.0051	0.0391	-0.0378	-0.0015	0.0219	25.9971	-26.4561	16.5509
39	15.2698	3.8086	-1.7302	4.9399	-1.3956	4.926	-0.2443	-0.1685	0.0119	-0.4078	-0.5331	-0.7269	0.3855	0.6129	0.7773	-0.0117	0.0917	0.15	0.0201	0.1673	0.1873	38.8493	-20.6725	15.9433
40	9.4206	-0.4044	1.7465	2.5035	-0.3113	2.4931	-0.3389	-0.0954	-0.4095	-0.4228	0.0615	-0.1103	0.1516	-0.053	0.2774	0.0321	0.016	0.0187	-0.0263	0.0118	0.0764	27.1876	-20.1992	17.9889

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	5 - 10	8 - 13
2	X-RAY DIFFRACTION	2	A	A	11 - 16	14 - 19
3	X-RAY DIFFRACTION	3	A	A	17 - 20	20 - 23
4	X-RAY DIFFRACTION	4	A	A	21 - 35	24 - 38
5	X-RAY DIFFRACTION	5	A	A	36 - 41	39 - 44
6	X-RAY DIFFRACTION	6	A	A	42 - 54	45 - 57
7	X-RAY DIFFRACTION	7	A	A	55 - 61	58 - 64
8	X-RAY DIFFRACTION	8	A	A	62 - 68	65 - 71
9	X-RAY DIFFRACTION	9	A	A	69 - 78	72 - 81
10	X-RAY DIFFRACTION	10	A	A	79 - 88	82 - 91
11	X-RAY DIFFRACTION	11	B	B	6 - 13	9 - 16
12	X-RAY DIFFRACTION	12	B	B	14 - 20	17 - 23
13	X-RAY DIFFRACTION	13	B	B	21 - 34	24 - 37
14	X-RAY DIFFRACTION	14	B	B	35 - 39	38 - 42
15	X-RAY DIFFRACTION	15	B	B	40 - 47	43 - 50
16	X-RAY DIFFRACTION	16	B	B	48 - 53	51 - 56
17	X-RAY DIFFRACTION	17	B	B	54 - 61	57 - 64
18	X-RAY DIFFRACTION	18	B	B	62 - 73	65 - 76
19	X-RAY DIFFRACTION	19	B	B	74 - 78	77 - 81
20	X-RAY DIFFRACTION	20	B	B	79 - 87	82 - 90
21	X-RAY DIFFRACTION	21	C	C	7 - 12	10 - 15
22	X-RAY DIFFRACTION	22	C	C	13 - 17	16 - 20
23	X-RAY DIFFRACTION	23	C	C	18 - 27	21 - 30
24	X-RAY DIFFRACTION	24	C	C	28 - 41	31 - 44
25	X-RAY DIFFRACTION	25	C	C	42 - 51	45 - 54
26	X-RAY DIFFRACTION	26	C	C	52 - 57	55 - 60
27	X-RAY DIFFRACTION	27	C	C	58 - 62	61 - 65
28	X-RAY DIFFRACTION	28	C	C	63 - 69	66 - 72
29	X-RAY DIFFRACTION	29	C	C	70 - 78	73 - 81
30	X-RAY DIFFRACTION	30	C	C	79 - 87	82 - 90
31	X-RAY DIFFRACTION	31	D	D	7 - 13	10 - 16
32	X-RAY DIFFRACTION	32	D	D	14 - 17	17 - 20
33	X-RAY DIFFRACTION	33	D	D	18 - 27	21 - 30
34	X-RAY DIFFRACTION	34	D	D	28 - 37	31 - 40
35	X-RAY DIFFRACTION	35	D	D	38 - 43	41 - 46
36	X-RAY DIFFRACTION	36	D	D	44 - 51	47 - 54
37	X-RAY DIFFRACTION	37	D	D	52 - 57	55 - 60
38	X-RAY DIFFRACTION	38	D	D	58 - 69	61 - 72
39	X-RAY DIFFRACTION	39	D	D	70 - 78	73 - 81
40	X-RAY DIFFRACTION	40	D	D	79 - 87	82 - 90

-
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

-
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