PDB-3oug: Crystal structure of cleaved L-aspartate-alpha-decarboxylase from...

ID or keywords:

Entry

Database: PDB / ID: 3oug

Title

Crystal structure of cleaved L-aspartate-alpha-decarboxylase from Francisella tularensis

Components

Aspartate 1-decarboxylase

Keywords

LYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / double-psi beta barrel / Aspartic alpha-decarboxylase / L-aspartate 1-carboxy-lyase (beta-alanine-forming) / pantothenate biosynthesis

Function / homology

Function and homology information

alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / cytosol
Similarity search - Function

Biological species

Francisella tularensis subsp. tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / SAD with molecular replacement / Resolution: 1.55 Å

Authors

Nocek, B. / Gu, M. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal structure of cleaved L-aspartate-alpha-decarboxylase from Francisella tularensis
Authors: Nocek, B. / Gu, M. / Papazisi, L. / Anderson, W. / Joachimiak, A.

History

Deposition	Sep 14, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 20, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3oug.cif.gz	388.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3oug.ent.gz	325.9 KB	Display	PDB format
PDBx/mmJSON format	3oug.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3oug_validation.pdf.gz	496.7 KB	Display	wwPDB validaton report
Full document	3oug_full_validation.pdf.gz	507.2 KB	Display
Data in XML	3oug_validation.xml.gz	44.4 KB	Display
Data in CIF	3oug_validation.cif.gz	63.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ou/3oug ftp://data.pdbj.org/pub/pdb/validation_reports/ou/3oug	HTTPS FTP

-
Related structure data

Related structure data	2c45S S: Starting model for refinement
Similar structure data	5tik-3 2amt-2 5kk7-2 2amt-1 1gx1-d 1knj-1 5tik-1 5tik-2 4ayr-d 1h48-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: idp02730

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#80 - Aug 2006 AAA+ Proteases similarity (1) #144 - Dec 2011 Complex I similarity (1) #167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Aspartate 1-decarboxylase

B: Aspartate 1-decarboxylase

C: Aspartate 1-decarboxylase

E: Aspartate 1-decarboxylase

F: Aspartate 1-decarboxylase

G: Aspartate 1-decarboxylase

H: Aspartate 1-decarboxylase

I: Aspartate 1-decarboxylase

hetero molecules

103 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate 1-decarboxylase

B: Aspartate 1-decarboxylase

C: Aspartate 1-decarboxylase

E: Aspartate 1-decarboxylase

hetero molecules

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

2

F: Aspartate 1-decarboxylase

G: Aspartate 1-decarboxylase

H: Aspartate 1-decarboxylase

I: Aspartate 1-decarboxylase

hetero molecules

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

3

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	79.934, 80.525, 85.025
Angle α, β, γ (deg.)	90.00, 104.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Aspartate 1-decarboxylase / Aspartate alpha-decarboxylase / Aspartate 1-decarboxylase beta chain / Aspartate 1-decarboxylase alpha chain Mass: 12709.223 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: SCHU S4 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q5NF56, aspartate 1-decarboxylase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 891 / 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: 2.61 Å³/Da / Density % sol: 52.83 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris, 25% PeG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2009 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.55→40 Å / Num. all: 151160 / Num. obs: 150740 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / R_merge(I) obs: 0.071 / Net I/σ(I): 27.6
Reflection shell	Resolution: 1.55→1.58 Å / R_merge(I) obs: 0.663 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
Auto-Rickshaw		phasing
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure: SAD with molecular replacement
Starting model: 2C45

2c45

Resolution: 1.55→28.66 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.954 / SU B: 2.989 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19704	972	6 %	RANDOM
R_work	0.17179	-	-	-
all	0.18	150301	-	-
obs	0.17196	149429	99.44 %	-

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: 17.715 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	-0.02 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→28.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6662	0	44	891	7597

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6972
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4742
X-RAY DIFFRACTION	r_angle_refined_deg	1.51	1.993	9460
X-RAY DIFFRACTION	r_angle_other_deg	1.066	3	11800
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.328	5	906
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.997	26.138	290
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.221	15	1372
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.872	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1161
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	7513
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1182
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	1.028	1.5	4351
X-RAY DIFFRACTION	r_mcbond_other	0.193	1.5	1743
X-RAY DIFFRACTION	r_mcangle_it	1.92	2	7141
X-RAY DIFFRACTION	r_scbond_it	2.646	3	2621
X-RAY DIFFRACTION	r_scangle_it	4.555	4.5	2284
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	73	-
R_work	0.3	10626	-
obs	-	-	96.65 %

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	0.2075	1.2353	-0.6529	8.4214	-1.7695	6.3812	-0.0432	-0.0102	-0.0032	-0.4673	-0.0216	0.0316	-0.2046	0.0108	0.0648	0.221	-0.0212	-0.0464	0.1804	-0.0436	0.086	42.887	34.6726	3.1402
2	0.1369	0.0417	0.3297	1.5979	0.4889	1.1178	0.0043	0.0296	-0.0917	-0.1329	0.11	-0.1848	0.0058	0.092	-0.1143	0.159	0.0118	0.0233	0.1293	-0.0344	0.1682	56.3476	23.3724	20.7955
3	2.5783	-1.1896	0.9011	1.8277	-0.0323	3.4703	0.0517	0.2053	-0.1169	-0.26	-0.0525	-0.0423	0.0989	0.187	0.0008	0.2156	0.0312	0.0351	0.1327	-0.0498	0.1018	56.3733	20.0066	10.74
4	1.0966	0.2499	-1.172	0.9889	-0.5795	2.9175	0.0036	0.0892	-0.0943	-0.1744	0.0074	-0.0523	0.0485	0.0544	-0.011	0.1633	0.002	-0.0144	0.1408	-0.0267	0.1433	51.7784	28.0101	16.8184
5	3.4937	-1.0639	-2.1084	1.1227	0.1163	2.082	0.0855	0.1087	0.0624	-0.2305	-0.0043	-0.0019	0.0046	0.1075	-0.0812	0.1665	-0.0066	-0.0074	0.1582	-0.0241	0.1058	55.6533	30.0118	16.2112
6	1.1071	-0.6527	-1.4374	10.6624	4.3055	4.9827	0.0762	0.1471	-0.1727	-0.2768	-0.0817	-0.2464	0.1878	0.0327	0.0055	0.1913	0.0284	-0.0139	0.1411	-0.0231	0.1538	59.4005	16.361	16.3443
7	2.4146	2.8502	-0.3153	4.1531	-0.3887	0.0464	0.0057	0.0617	-0.0719	-0.0735	-0.0019	-0.1275	0.0223	-0.0102	-0.0037	0.1373	0.0153	-0.001	0.1523	-0.0057	0.131	57.7972	27.9257	26.5264
8	2.1167	0.3514	-0.2515	0.0815	0.38	7.9597	-0.0631	0.1176	-0.1105	0.0039	0.0027	-0.0134	0.3181	-0.1163	0.0604	0.2002	-0.0115	-0.0264	0.113	-0.0199	0.1579	47.916	23.977	18.8136
9	1.3515	-0.5427	0.9121	4.2416	-0.8252	1.8394	-0.1957	0.0869	-0.2999	-0.4877	-0.0485	-0.106	-0.2244	0.117	0.2442	0.234	-0.0032	0.0018	0.16	-0.0274	0.2357	43.0055	34.1184	0.392
10	5.1896	-4.5607	5.8614	4.1935	-6.1458	12.1932	0.0446	0.1804	-0.3328	-0.1355	-0.0675	0.2275	0.3201	-0.2438	0.0229	0.2934	-0.074	-0.0566	0.1256	-0.0869	0.114	42.0079	21.2047	7.3843
11	5.962	-1.3745	-0.8007	0.3918	0.7959	5.2255	0.0918	0.3245	-0.0287	-0.0932	-0.0445	0.0089	-0.3715	0.3764	-0.0474	0.4344	0.0076	-0.0992	0.1657	-0.0134	0.027	43.9189	47.7055	2.9108
12	1.648	0.8283	-0.9665	1.5512	-1.4184	1.7604	-0.0028	0.1062	0.1201	-0.0854	0.0301	0.2582	-0.0877	-0.1273	-0.0273	0.138	0.0065	-0.0651	0.162	0.0005	0.168	29.3331	41.9055	17.9574
13	2.6646	-2.1966	2.0606	1.8841	-1.4448	2.4726	0.3249	0.1655	-0.3905	-0.2585	-0.1129	0.3513	0.2862	0.2102	-0.212	0.2033	-0.0627	-0.0333	0.1372	-0.044	0.2467	35.8428	24.1502	23.474
14	2.5428	0.527	-1.4784	3.3136	-1.7944	1.5892	-0.0427	0.3038	-0.0865	-0.3481	0.0375	0.2101	0.1721	-0.2389	0.0052	0.1763	-0.0181	-0.1425	0.1995	-0.091	0.1872	27.7829	35.1289	9.8414
15	0.4368	-0.1499	-0.4772	1.2356	1.3205	3.5322	0.0066	0.0645	-0.0602	-0.1509	0.0035	0.1121	0.0183	-0.0552	-0.0101	0.1499	-0.0025	-0.0329	0.1429	0.0082	0.1421	36.7842	38.1665	17.0321
16	2.2249	0.4885	-0.6211	13.453	7.1101	4.3153	-0.0269	0.0595	0.0179	0.0022	0.1722	-0.0571	0.0688	0.244	-0.1453	0.1889	0.0407	-0.015	0.1982	-0.0239	0.1338	42.0636	38.6627	20.0174
17	7.802	-0.1645	-0.6946	1.7262	0.3635	2.3135	-0.0163	0.2703	-0.301	-0.3249	0.028	0.2745	0.0804	-0.298	-0.0117	0.172	-0.0373	-0.0753	0.1383	-0.0085	0.1623	27.5033	29.4587	13.6531
18	2.9587	-1.8915	0.6325	1.3632	-0.3374	0.1648	0.0084	0.0836	-0.1064	-0.0914	0.0112	0.0908	-0.0344	0.0527	-0.0196	0.1429	-0.0239	-0.0171	0.1509	0.0016	0.1501	37.1673	30.9361	24.6422
19	1.9178	1.0847	-3.0565	1.5971	-1.2181	5.907	-0.0276	0.136	0.0524	-0.2909	0.088	0.0952	-0.1899	-0.1619	-0.0604	0.1982	0.0027	-0.0711	0.1554	-0.0165	0.1345	37.0834	43.8113	11.0767
20	4.5982	3.8503	-5.7769	3.8341	-3.3996	12.046	0.0602	0.2885	0.3177	-0.2636	0.0324	0.4962	-0.6353	-0.587	-0.0927	0.2157	0.0937	-0.1769	0.2691	-0.0251	0.1868	29.053	47.1371	8.6475
21	28.3624	-4.1358	10.6577	1.0588	-2.4582	5.8013	-0.0875	0.6859	-0.3992	-0.0945	-0.0033	-0.0658	0.1511	0.0648	0.0908	0.3354	0.0058	0.057	0.1925	-0.0477	0.0429	53.9937	33.2314	2.9363
22	1.4498	0.5181	0.8372	1.4653	1.0162	1.2972	0.0159	0.1966	-0.0212	-0.1184	0.0039	-0.1638	0.0043	0.1002	-0.0198	0.1274	0.0027	0.0528	0.1806	0.0014	0.1374	68.9638	40.6024	17.2643
23	0.2192	0.5195	0.2433	4.4394	3.3004	2.5851	0.2993	0.1012	0.0194	-0.4634	0.2029	-0.6863	-0.6006	0.0182	-0.5022	0.5487	0.1336	0.1993	0.0632	0.0648	0.4451	61.9082	57.282	24.3126
24	1.1256	0.1782	1.2523	2.9844	1.6814	2.1453	0.0437	0.1736	0.0995	-0.3202	0.0148	-0.2783	-0.1407	0.2055	-0.0585	0.1486	-0.0097	0.1022	0.2355	0.0229	0.1328	70.4906	46.3453	10.0928
25	0.6789	-0.506	0.614	1.2715	-1.5726	3.6543	0.0375	0.1098	0.058	-0.1449	-0.0106	-0.1185	-0.0546	0.0299	-0.027	0.1503	-0.001	0.0326	0.1551	-0.0108	0.1444	61.9683	42.9471	16.93
26	0.9798	-0.0059	0.4991	2.0155	-0.5678	0.8212	0.0244	0.2514	0.1119	-0.3117	0.0003	-0.0462	-0.0225	0.0815	-0.0247	0.1822	0.014	0.0536	0.1852	0.0099	0.1016	65.0402	48.5344	15.4721
27	11.0822	-2.0251	-2.9998	4.4137	0.3485	1.1184	0.0888	-0.1007	0.2697	-0.0632	0.087	-0.2164	0.0603	-0.0093	-0.1758	0.1334	-0.014	0.0366	0.1688	0.0091	0.1454	68.7289	50.1552	20.045
28	2.2487	-2.0376	-0.1251	2.3424	-0.0871	0.0945	0.0161	0.0007	0.0433	-0.0688	0.0161	-0.0405	0.0251	-0.0071	-0.0322	0.1345	-0.0021	0.0057	0.1404	0.001	0.1329	61.8802	48.333	27.3332
29	2.8919	0.4142	2.9342	0.8198	0.8635	5.6203	0.1419	0.2252	-0.1726	-0.3075	0.0124	-0.1529	0.2606	0.0459	-0.1544	0.2342	0.0245	0.0539	0.1736	0.0087	0.1268	59.8797	36.0989	7.2807
30	5.1767	3.5844	8.139	4.78	3.3695	15.0454	0.0779	0.1552	-0.2766	-0.3901	-0.0679	-0.6184	0.5207	0.3691	-0.0099	0.1934	0.1052	0.1017	0.3016	-0.046	0.13	69.3154	34.1629	8.3008
31	0.862	-1.0599	-0.8661	1.953	0.8202	1.8828	0.0662	0.1416	0.1417	-0.3133	-0.0805	-0.05	-0.018	0.0221	0.0143	0.1928	-0.0123	-0.0098	0.1625	0.0657	0.1102	52.0896	54.8255	12.3616
32	5.9207	5.136	-2.0074	6.7737	-1.0155	0.9085	-0.0753	0.5163	0.6997	-0.3866	0.3206	0.5748	-0.0685	-0.222	-0.2453	0.1658	0.0645	-0.0546	0.241	0.0613	0.2122	32.1997	52.6851	25.2799
33	1.398	-0.0119	-0.8031	1.9621	-0.2861	2.3376	-0.0089	0.1063	0.0488	-0.2538	0.0034	0.0912	-0.1206	-0.0164	0.0055	0.2037	0.0071	-0.0502	0.1319	0.0341	0.116	43.3223	61.904	10.6511
34	1.048	0.1287	1.5238	1.0827	0.2401	3.1605	-0.0225	0.0507	0.0448	-0.2103	0.0065	0.0963	-0.0251	0.0173	0.016	0.1612	-0.002	-0.0015	0.1256	0.0121	0.135	46.9016	53.4097	16.5005
35	9.0491	-0.5333	6.3536	1.4545	-0.1513	4.5033	0.1719	-0.0315	-0.1945	-0.1744	-0.032	0.0535	0.1219	-0.0118	-0.1399	0.1807	-0.0225	-0.0082	0.1765	0.0118	0.1023	45.5131	48.4108	18.5935
36	0.11	-0.738	0.3394	7.0766	-0.7879	3.4012	0.0282	0.0112	0.0064	-0.2297	-0.0369	0.4385	-0.2236	-0.058	0.0086	0.1686	0.0254	-0.0272	0.1278	0.0583	0.2679	38.6992	63.6912	15.0992
37	2.1885	2.923	0.335	4.1303	0.3459	0.1049	-0.04	0.0734	0.0346	-0.0909	0.057	0.099	-0.02	0.0139	-0.017	0.138	0.0186	-0.0099	0.1571	0.0014	0.1385	40.9868	53.0995	26.4581
38	0.4154	-0.844	-0.4147	1.816	1.033	5.3189	0.0726	0.0931	0.0724	-0.2278	-0.1047	-0.0628	0.0986	0.1889	0.0321	0.2049	-0.018	-0.0002	0.1895	0.0508	0.1347	52.2696	52.3831	10.9358
39	6.626	-9.023	-7.9617	15.33	11.3518	9.652	0.2333	-1.0154	0.9028	-2.5106	1.0434	-1.7399	-0.7512	1.1802	-1.2767	1.3993	0.069	0.3858	0.5614	-0.0542	0.2139	60.2194	49.8045	-3.1223
40	4.557	-4.8096	-5.2536	5.3991	4.4692	16.5434	-0.0117	0	0.6014	-0.238	0.0369	-0.554	-0.2169	0.5744	-0.0252	0.3676	-0.1042	-0.1369	0.1221	0.1555	0.2777	55.0528	62.9543	11.8202
41	15.0893	1.0981	-5.6484	0.1127	-0.8704	9.1758	0.0189	-0.29	0.243	0.0251	0.0149	-0.0023	-0.0977	-0.427	-0.0338	0.2232	0.0033	-0.0473	0.144	-0.0001	0.1213	55.6079	46.3735	60.6622
42	0.77	-0.2302	0.2203	0.3997	0.3328	0.9265	0.0314	-0.0267	-0.1003	0.0605	-0.0154	-0.0081	0.0951	-0.0386	-0.0159	0.1201	0.0118	-0.0003	0.1353	0.005	0.1491	64.1003	30.271	44.0923
43	4.2351	-0.033	1.6499	1.6657	-0.0008	3.2953	0.048	-0.0111	-0.173	0.0766	0.0108	0.0889	0.2007	-0.1436	-0.0589	0.1298	0.0061	0.0052	0.1401	0.0074	0.1425	64.538	25.3778	48.2377
44	3.3479	-1.5833	-2.5282	4.5562	2.8805	3.8422	-0.1138	-0.1682	0.0696	0.1529	0.1618	-0.2603	0.0849	0.1486	-0.048	0.133	0.0111	-0.026	0.1449	0.0014	0.1504	70.074	31.1557	55.8608
45	0.6822	0.5263	-1.0451	1.6987	-2.0682	4.1967	0.0024	-0.0405	-0.0469	0.0339	-0.0109	-0.0306	0.0263	-0.0034	0.0085	0.1118	0.0004	-0.0092	0.1338	-0.006	0.1389	60.4604	34.8022	46.0234
46	1.2978	-0.8738	0.5213	11.8613	-7.801	5.1352	-0.0479	-0.0305	0.058	0.1398	0.0711	0.0396	-0.0837	-0.028	-0.0233	0.1263	-0.0203	-0.007	0.1632	-0.0071	0.1402	55.8571	33.9986	46.3655
47	6.6247	-2.4924	-0.2549	2.4316	-0.0248	1.2792	-0.0286	-0.1332	-0.2199	0.1231	0.0287	-0.0449	0.0798	0.077	-0.0001	0.1374	0.0084	-0.0158	0.1215	0.0025	0.152	69.5534	23.5221	49.595
48	4.2056	0.8175	0.4784	0.1754	0.065	0.1126	0.0443	-0.0565	-0.0347	0.0017	0	0.0059	-0.0158	-0.0331	-0.0444	0.1317	0.0082	0.0006	0.1345	-0.006	0.1485	59.5235	28.2788	38.2523
49	1.3331	-1.044	-2.1598	1.5432	1.5443	4.6118	0.0116	-0.0875	0.1144	0.1633	0.0854	-0.0649	-0.0732	0.1237	-0.097	0.1367	-0.0071	-0.0231	0.1417	0.0078	0.1551	61.7832	40.6909	52.7567
50	2.8806	-3.2804	-4.8019	5.9512	5.1195	10.6764	0.0058	-0.2551	0.1937	0.2174	0.0307	-0.3389	-0.1636	0.2947	-0.0366	0.0882	-0.0174	-0.0855	0.1902	-0.0277	0.1498	70.3901	41.778	55.3225
51	17.0227	0.1943	5.2763	0.2756	1.2113	8.4658	-0.1137	-0.4249	-0.2636	0.1473	0.1156	0.0466	0.0876	0.3821	-0.0019	0.2292	0.0217	0.0381	0.1547	0.0066	0.1261	43.3212	34.3392	60.6623
52	0.8362	-0.4603	0.2433	2.1733	-1.4413	1.4246	-0.0078	-0.0773	-0.0491	0.0272	0.0354	0.1189	0.0031	-0.0672	-0.0276	0.1052	0.0071	0.0173	0.1425	0.0011	0.1472	30.563	45.3278	46.2393
53	2.1338	1.7645	-0.2922	1.9087	-1.0074	1.3459	0.1302	-0.0111	0.3494	0.2719	-0.0678	0.3015	-0.3046	0.0878	-0.0624	0.1523	0.0077	0.02	0.1302	-0.0285	0.2555	41.7734	60.5312	40.0482
54	1.1431	-0.5513	0.4179	2.5668	-1.1639	1.2337	-0.0524	-0.1182	-0.0697	0.1659	0.0561	0.1947	-0.0907	-0.09	-0.0037	0.1321	0.0109	0.0133	0.1417	-0.0091	0.1512	30.2651	51.3779	53.2515
55	0.6062	0.3084	0.695	1.1465	1.3865	3.2178	-0.0074	-0.0604	0.0558	0.0666	-0.0193	0.0682	-0.0162	-0.0069	0.0267	0.1139	0.0002	0.0153	0.1323	0.006	0.1388	37.6333	45.9621	47.1418
56	2.5443	2.2694	1.1549	9.5169	5.8166	3.6113	0.0375	-0.0425	-0.0325	0.0065	0.0587	-0.1076	-0.0331	0.0995	-0.0963	0.126	-0.0408	0.0027	0.1879	0.0181	0.1414	42.8432	43.9375	43.5012
57	6.4847	-1.808	0.8661	1.12	-0.296	0.65	-0.0395	-0.1379	0.1594	0.1303	0.041	0.0585	-0.0562	-0.0401	-0.0015	0.1384	0.0102	0.0191	0.127	-0.0001	0.158	31.2345	56.6115	50.0202
58	3.2146	0.7811	-0.2898	0.1973	-0.034	0.225	0.0475	-0.0532	0.0287	0.0088	-0.0099	0.0069	0.0247	0.0293	-0.0377	0.1268	0.0073	0.0019	0.1356	0.0071	0.1384	39.3138	52.6798	38.7086
59	1.4036	-1.0605	2.3189	1.5809	-1.6524	4.8301	0.0234	-0.073	-0.1597	0.1382	0.0765	0.0731	0.0543	-0.0984	-0.0999	0.1273	-0.0044	0.0295	0.1407	0.0035	0.1611	37.0925	40.1598	52.1444
60	3.0924	-3.5726	4.8708	5.9158	-5.074	10.0598	-0.0007	-0.2851	-0.071	0.2611	0.0616	0.2366	0.1881	-0.2917	-0.061	0.1029	-0.024	0.0895	0.1947	0.0211	0.1344	29.8654	38.173	57.1915
61	0.5143	2.6213	0.8679	13.6619	5.8416	9.7568	0.0955	-0.0238	-0.09	0.3136	-0.0779	-0.3584	-0.4661	-0.0062	-0.0176	0.1695	-0.0116	-0.0264	0.1787	0.0587	0.143	55.637	33.7856	60.3328
62	0.4764	0.0931	0.4449	1.1586	-0.4098	1.1931	-0.0089	-0.0595	0.0071	0.0342	0.0361	0.1316	-0.0234	-0.0962	-0.0272	0.115	-0.0163	0.0121	0.1293	0.0058	0.1485	39.0355	25.5652	43.4423
63	2.3001	0.9723	1.0206	1.9864	-0.1363	2.6654	0.0443	-0.1371	-0.1348	0.1323	-0.0006	-0.0219	0.0275	-0.1146	-0.0436	0.1232	-0.0119	0.016	0.1367	0.0036	0.1445	38.0593	21.868	52.8232
64	1.5186	-0.4365	-1.8985	0.8279	1.0737	4.3018	-0.0113	-0.0339	-0.0322	0.0477	0.0089	0.0501	-0.0155	-0.0249	0.0024	0.1176	0.0004	-0.0047	0.1228	0.0113	0.14	44.1882	29.0418	45.7339
65	6.8758	0.6827	-5.1371	2.048	-0.4458	3.8408	0.1635	-0.0888	0.0911	0.0119	-0.0919	-0.0479	-0.1202	0.0548	-0.0716	0.1218	0.007	-0.0103	0.1576	0.0031	0.1381	42.3637	33.2287	47.1199
66	1.6032	2.0826	0.1246	6.4585	0.4143	1.7499	0.0449	-0.1045	-0.0775	0.1126	-0.064	0.1712	0.0563	-0.0506	0.0191	0.1003	-0.0128	0.0009	0.1489	0.0201	0.1624	32.3656	19.1996	49.4313
67	0.2726	-1.0195	0.1302	3.9086	-0.6514	0.3981	-0.0114	0.0025	0.0019	0.0455	0.027	0.0341	-0.0295	-0.0051	-0.0156	0.1199	-0.0096	-0.0018	0.1389	-0.0006	0.1586	37.8739	29.3902	38.0121
68	1.5441	1.5694	2.3909	1.9802	2.6563	7.1238	0.0024	-0.1344	-0.0412	0.0297	0.0174	-0.0873	-0.0115	0.0682	-0.0198	0.123	0.0085	0.0027	0.1452	0.0241	0.149	49.7429	28.015	52.6656
69	3.7184	10.572	8.0202	30.6201	21.3634	22.4414	0.7513	-0.0471	-0.4987	2.3131	-0.0052	-1.2725	0.5474	0.2994	-0.7461	0.4807	-0.0729	-0.21	0.4525	0.4008	0.4438	57.3873	27.5864	67.2091
70	7.0701	3.5882	5.3895	3.0447	4.5453	11.7596	0.1518	-0.0326	-0.4527	0.2867	-0.0018	-0.241	0.4584	0.1725	-0.15	0.1818	0.0142	-0.0144	0.0652	0.0621	0.1882	49.2491	17.1649	52.0607
71	1.0472	2.5498	-1.4963	9.2101	-3.0886	7.1517	0.0859	-0.0661	0.1902	0.2604	0.009	0.3396	0.3965	-0.1052	-0.0949	0.1518	-0.0004	0.0101	0.17	-0.0272	0.1187	43.304	46.676	60.3617
72	0.5232	0.0783	-0.4203	1.118	0.3675	0.9912	-0.0031	-0.0618	-0.0146	0.0262	0.0249	-0.1146	0.0233	0.0843	-0.0219	0.1165	-0.0153	-0.0064	0.1287	-0.0024	0.1345	59.8569	55.0919	43.6589
73	1.7288	0.8656	-0.6355	1.1988	-0.4246	1.9791	0.0468	-0.0969	0.07	0.1156	-0.0101	0.0052	-0.0255	0.0736	-0.0367	0.1263	-0.0143	-0.013	0.1395	-0.0034	0.1389	61.0447	57.9246	53.0956
74	1.6855	-0.6615	1.9528	1.0205	-1.2729	4.4555	-0.0214	-0.022	0.0231	0.0622	0.0172	-0.0259	-0.0001	0.0302	0.0043	0.117	-0.0017	0.0096	0.1175	-0.0094	0.1276	54.2992	51.4704	45.0313
75	7.0686	0.6423	5.3672	1.6608	0.6739	4.0976	0.1251	-0.0925	-0.0665	0.0196	-0.0809	0.0677	0.0907	-0.0711	-0.0443	0.1281	0.0051	0.01	0.1541	-0.0031	0.1326	56.5394	47.3885	47.2387
76	1.0746	1.7842	0.5892	4.9834	0.4583	1.9424	0.0082	-0.0899	0.0632	0.0637	-0.0183	-0.2064	-0.0856	0.0747	0.0101	0.1054	-0.0109	0.0056	0.1492	-0.0145	0.1528	65.8852	60.6962	48.6621
77	0.9819	-2.1219	-0.0062	4.6275	-0.0045	0.664	-0.0395	-0.0348	0.0005	0.0307	0.0504	-0.0444	0.0121	-0.0045	-0.0109	0.1172	-0.0087	0.0076	0.1479	0.0039	0.1434	60.8277	50.5221	37.4765
78	1.4796	1.2124	-2.1285	1.1878	-2.3317	7.0067	0.0166	-0.1226	-0.0124	-0.032	-0.0021	0.0774	0.0508	0.0153	-0.0145	0.1249	-0.0029	0.0018	0.1382	-0.0064	0.1456	50.5257	53.4457	50.6187
79	15.367	12.6068	-17.8886	87.2822	-17.6961	20.9455	0.5329	-0.7075	-0.8966	4.381	-1.4284	3.5286	-0.7535	0.8927	0.8955	0.3534	-0.1944	0.2645	0.4846	-0.1456	0.3441	40.6148	50.2499	67.6675
80	6.2311	4.0553	-6.8285	3.3894	-4.6426	13.5206	0.0408	-0.0184	0.3137	0.3478	-0.0541	0.1623	-0.3733	-0.2084	0.0134	0.1934	-0.0019	0.0225	0.0925	-0.0697	0.1503	49.1416	62.493	53.5453

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 7
2	X-RAY DIFFRACTION	2	A	8 - 22
3	X-RAY DIFFRACTION	3	A	23 - 39
4	X-RAY DIFFRACTION	4	A	40 - 53
5	X-RAY DIFFRACTION	5	A	54 - 62
6	X-RAY DIFFRACTION	6	A	63 - 72
7	X-RAY DIFFRACTION	7	A	73 - 84
8	X-RAY DIFFRACTION	8	A	85 - 89
9	X-RAY DIFFRACTION	9	A	90 - 98
10	X-RAY DIFFRACTION	10	A	99 - 109
11	X-RAY DIFFRACTION	11	B	1 - 7
12	X-RAY DIFFRACTION	12	B	8 - 15
13	X-RAY DIFFRACTION	13	B	16 - 26
14	X-RAY DIFFRACTION	14	B	27 - 39
15	X-RAY DIFFRACTION	15	B	40 - 53
16	X-RAY DIFFRACTION	16	B	54 - 58
17	X-RAY DIFFRACTION	17	B	59 - 69
18	X-RAY DIFFRACTION	18	B	70 - 81
19	X-RAY DIFFRACTION	19	B	82 - 98
20	X-RAY DIFFRACTION	20	B	99 - 109
21	X-RAY DIFFRACTION	21	C	1 - 6
22	X-RAY DIFFRACTION	22	C	7 - 17
23	X-RAY DIFFRACTION	23	C	18 - 22
24	X-RAY DIFFRACTION	24	C	26 - 39
25	X-RAY DIFFRACTION	25	C	40 - 53
26	X-RAY DIFFRACTION	26	C	54 - 67
27	X-RAY DIFFRACTION	27	C	68 - 73
28	X-RAY DIFFRACTION	28	C	74 - 84
29	X-RAY DIFFRACTION	29	C	85 - 98
30	X-RAY DIFFRACTION	30	C	99 - 109
31	X-RAY DIFFRACTION	31	E	1 - 17
32	X-RAY DIFFRACTION	32	E	18 - 23
33	X-RAY DIFFRACTION	33	E	26 - 38
34	X-RAY DIFFRACTION	34	E	39 - 53
35	X-RAY DIFFRACTION	35	E	54 - 59
36	X-RAY DIFFRACTION	36	E	60 - 71
37	X-RAY DIFFRACTION	37	E	72 - 84
38	X-RAY DIFFRACTION	38	E	85 - 95
39	X-RAY DIFFRACTION	39	E	96 - 101
40	X-RAY DIFFRACTION	40	E	102 - 109
41	X-RAY DIFFRACTION	41	F	1 - 6
42	X-RAY DIFFRACTION	42	F	7 - 22
43	X-RAY DIFFRACTION	43	F	23 - 31
44	X-RAY DIFFRACTION	44	F	32 - 39
45	X-RAY DIFFRACTION	45	F	40 - 54
46	X-RAY DIFFRACTION	46	F	55 - 59
47	X-RAY DIFFRACTION	47	F	60 - 69
48	X-RAY DIFFRACTION	48	F	70 - 82
49	X-RAY DIFFRACTION	49	F	83 - 98
50	X-RAY DIFFRACTION	50	F	99 - 109
51	X-RAY DIFFRACTION	51	G	1 - 6
52	X-RAY DIFFRACTION	52	G	7 - 17
53	X-RAY DIFFRACTION	53	G	18 - 23
54	X-RAY DIFFRACTION	54	G	26 - 38
55	X-RAY DIFFRACTION	55	G	39 - 53
56	X-RAY DIFFRACTION	56	G	54 - 58
57	X-RAY DIFFRACTION	57	G	59 - 69
58	X-RAY DIFFRACTION	58	G	70 - 82
59	X-RAY DIFFRACTION	59	G	83 - 97
60	X-RAY DIFFRACTION	60	G	98 - 109
61	X-RAY DIFFRACTION	61	H	1 - 6
62	X-RAY DIFFRACTION	62	H	7 - 22
63	X-RAY DIFFRACTION	63	H	23 - 39
64	X-RAY DIFFRACTION	64	H	40 - 54
65	X-RAY DIFFRACTION	65	H	55 - 60
66	X-RAY DIFFRACTION	66	H	61 - 69
67	X-RAY DIFFRACTION	67	H	70 - 84
68	X-RAY DIFFRACTION	68	H	85 - 96
69	X-RAY DIFFRACTION	69	H	97 - 101
70	X-RAY DIFFRACTION	70	H	102 - 109
71	X-RAY DIFFRACTION	71	I	1 - 6
72	X-RAY DIFFRACTION	72	I	7 - 22
73	X-RAY DIFFRACTION	73	I	23 - 40
74	X-RAY DIFFRACTION	74	I	41 - 54
75	X-RAY DIFFRACTION	75	I	55 - 60
76	X-RAY DIFFRACTION	76	I	61 - 71
77	X-RAY DIFFRACTION	77	I	72 - 84
78	X-RAY DIFFRACTION	78	I	85 - 94
79	X-RAY DIFFRACTION	79	I	95 - 100
80	X-RAY DIFFRACTION	80	I	101 - 109

-
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