PDB-5jh9: Crystal structure of prApe1

ID or keywords:

Entry

Database: PDB / ID: 5jh9

Title

Crystal structure of prApe1

Components

Vacuolar aminopeptidase 1

Keywords

HYDROLASE / Tetrahedral dodecamer

Function / homology

Function and homology information

aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / fungal-type vacuole / metalloaminopeptidase activity /

protein transport /

proteolysis / zinc ion binding / identical protein binding /

cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Noda, N.N. / Adachi, W. / Inagaki, F.

Citation

Journal: Cell Rep / Year: 2016
Title: Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates
Authors: Yamasaki, A. / Watanabe, Y. / Adachi, W. / Suzuki, K. / Matoba, K. / Kirisako, H. / Kumeta, H. / Nakatogawa, H. / Ohsumi, Y. / Inagaki, F. / Noda, N.N.

History

Deposition	Apr 20, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2016	Group: Database references
Revision 1.2	Feb 19, 2020	Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 8, 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 / pdbx_struct_conn_angle / struct_conn 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_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.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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5jh9.cif.gz	743 KB	Display	PDBx/mmCIF format
PDB format	pdb5jh9.ent.gz	619.2 KB	Display	PDB format
PDBx/mmJSON format	5jh9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jh/5jh9 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/5jh9	HTTPS FTP

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Related structure data

Related structure data	5jgeC 5jgfSC 5jhcC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4oiw-1 4oid-1 5jgf-1 3vat-1 8167 3wt4-1 5jm6-1 4dyo-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (7) #133 - Jan 2011 Nitric Oxide Synthase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Vacuolar aminopeptidase 1

B: Vacuolar aminopeptidase 1

C: Vacuolar aminopeptidase 1

D: Vacuolar aminopeptidase 1

hetero molecules

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

1

A: Vacuolar aminopeptidase 1

B: Vacuolar aminopeptidase 1

C: Vacuolar aminopeptidase 1

D: Vacuolar aminopeptidase 1

hetero molecules

A: Vacuolar aminopeptidase 1

B: Vacuolar aminopeptidase 1

C: Vacuolar aminopeptidase 1

D: Vacuolar aminopeptidase 1

hetero molecules

A: Vacuolar aminopeptidase 1

B: Vacuolar aminopeptidase 1

C: Vacuolar aminopeptidase 1

D: Vacuolar aminopeptidase 1

hetero molecules

defined by author&software
692 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	140.428, 140.428, 348.922
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Vacuolar aminopeptidase 1 / Aminopeptidase yscI / Leucine aminopeptidase IV / LAPIV / Lysosomal aminopeptidase III / ...Aminopeptidase yscI / Leucine aminopeptidase IV / LAPIV / Lysosomal aminopeptidase III / Polypeptidase / Vacuolar aminopeptidase I Mass: 57290.516 Da / Num. of mol.: 4 / Mutation: L11S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: APE1, API, LAP4, YSC1, YKL103C, YKL455 / Production host: Escherichia coli (E. coli) / References: UniProt: P14904, aminopeptidase I
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid Mass: 136.989 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆AsO₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 819 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.89 Å³/Da / Density % sol: 57.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50% (v/v) PEG 200, 200 mM Magnesium chloride, 100 mM sodium cacodylate

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 16, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→500 Å / Num. obs: 123984 / % possible obs: 100 % / Redundancy: 5.4 % / R_merge(I) obs: 0.045 / Net I/σ(I): 20.3
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 5 % / R_merge(I) obs: 0.19 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JGF

5jgf

Resolution: 2.1→44.79 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.936 / SU B: 7.623 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20737	13720	10 %	RANDOM
R_work	0.18065	-	-	-
obs	0.18332	123984	91.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 36.387 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.66 Å²	0.83 Å²	-0 Å²
2-	-	1.66 Å²	-0 Å²
3-	-	-	-5.38 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→44.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14619	0	48	819	15486

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	15003
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14210
X-RAY DIFFRACTION	r_angle_refined_deg	1.208	1.956	20375
X-RAY DIFFRACTION	r_angle_other_deg	0.892	3	32707
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.021	5	1892
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.136	24.268	656
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.094	15	2399
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.916	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	2256
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	17092
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3448
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	0.397	1.467	7592
X-RAY DIFFRACTION	r_mcbond_other	0.397	1.467	7591
X-RAY DIFFRACTION	r_mcangle_it	0.748	2.195	9476
X-RAY DIFFRACTION	r_mcangle_other	0.748	2.195	9477
X-RAY DIFFRACTION	r_scbond_it	0.351	1.46	7411
X-RAY DIFFRACTION	r_scbond_other	0.351	1.461	7412
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.415	2.192	10900
X-RAY DIFFRACTION	r_long_range_B_refined	5.584	12.292	17249
X-RAY DIFFRACTION	r_long_range_B_other	5.559	12.197	17177
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.099→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	954	-
R_work	0.223	8463	-
obs	-	-	85.1 %

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	7.8431	7.1449	1.1112	7.5685	2.4943	2.2525	-0.4103	0.7193	0.3016	-1.2496	0.5161	0.13	-1.2963	0.0162	-0.1058	0.8062	0.0569	-0.0884	0.704	0.1474	0.6149	-44.122	-81.461	-47.021
2	2.1088	-2.1945	-2.1606	3.7249	5.6408	11.4978	0.2626	0.2309	0.1776	-0.4841	-0.1786	0.1293	-0.447	-0.2571	-0.084	0.1664	0.0109	-0.1712	0.2496	0.0612	0.4293	-40.722	-75.798	-35.206
3	2.36	2.5196	1.3705	2.7433	1.7305	2.1562	0.0213	0.1678	0.241	-0.0252	0.1012	0.2238	-0.2631	-0.2071	-0.1226	0.1244	0.0447	-0.0966	0.2308	-0.0087	0.5395	-52.582	-89.498	-27.796
4	4.1505	0.6501	2.9024	3.0381	3.6036	8.3352	0.1156	0.0639	-0.254	-0.0657	-0.0481	0.3418	0.0102	-0.326	-0.0675	0.0531	-0.0396	-0.1229	0.2744	-0.0294	0.4134	-53.899	-97.564	-28.818
5	8.1374	-1.5295	4.6915	6.5044	-1.964	5.9186	0.3113	0.5697	-0.2922	-0.4632	-0.244	0.3825	0.4391	-0.2046	-0.0673	0.1291	-0.0571	-0.098	0.3035	-0.0571	0.2763	-49.521	-107.096	-38.86
6	0.1275	-0.1719	0.0313	0.8967	0.8888	1.3572	0.0476	0.0395	-0.0061	-0.1436	-0.1665	0.1491	-0.0746	-0.224	0.1189	0.054	-0.0329	-0.0656	0.1892	-0.0106	0.3796	-39.16	-86.548	-19.833
7	1.0316	0.1564	-0.386	3.1756	0.1256	0.5975	0.0526	0.0368	0.0521	0.0284	0.0477	-0.0294	0.0523	-0.1211	-0.1002	0.0428	0.0001	-0.0591	0.1153	0.0176	0.307	-34.174	-70.357	-9.277
8	5.9315	2.6124	-1.5238	5.2991	-0.9278	0.7748	0.0152	0.0613	-0.2259	0.0513	-0.0097	0.289	-0.1626	-0.2689	-0.0055	0.1032	0.0873	-0.0875	0.261	0.0343	0.3914	-52.629	-75.138	-14.094
9	2.57	2.1225	0.4639	6.8409	-2.5425	1.8358	-0.0829	0.0253	-0.2134	-0.2001	-0.0327	-0.339	0.0941	0.1201	0.1157	0.0999	0.0253	0.0029	0.1283	0.0116	0.288	-21.623	-65.952	-8.234
10	3.3372	0.8856	-0.1485	1.2311	0.2044	0.1456	-0.0319	-0.3494	0.3402	0.1135	0.0725	0.142	-0.0459	-0.0578	-0.0405	0.1215	0.106	0.003	0.2529	0.0471	0.3327	-45.514	-65.624	-2.842
11	5.0491	-1.3459	0.3742	2.1985	-0.101	8.666	-0.0006	-0.0304	0.185	0.0204	0.0488	0.2741	-0.3559	-0.1595	-0.0482	0.0557	0.0821	-0.0396	0.171	0.015	0.4097	-53.752	-70.691	-7.295
12	0.6926	0.0667	-0.1488	0.9363	-0.0682	0.0445	0.0172	0.1269	0.0188	-0.2283	-0.0145	0.2093	-0.0009	-0.06	-0.0027	0.1153	0.0133	-0.1076	0.1786	0.0109	0.3537	-36.261	-75.887	-27.4
13	5.5426	7.3353	2.3539	16.0757	3.3359	4.6427	-0.2669	0.3873	0.3879	-0.3656	0.1741	0.8895	0.1643	0.0381	0.0928	0.1524	0.0536	-0.1391	0.4635	-0.0295	0.3017	-48.336	-94.205	-42.414
14	1.2249	1.1977	0.9217	1.3414	0.6432	1.4356	-0.0405	-0.0618	-0.0104	-0.1065	-0.0219	0.122	-0.0504	-0.0612	0.0624	0.0812	-0.0453	-0.0906	0.1524	-0.0526	0.3964	-43.712	-98.688	-24.529
15	29.0579	-12.2873	15.3174	5.1961	-6.4776	8.0756	0.2129	-1.6885	-1.7798	-0.0895	0.7091	0.746	0.103	-0.8781	-0.922	0.3826	-0.1043	-0.1667	0.4623	-0.0488	0.6485	-53.11	-113.978	-32.216
16	0.6213	0.3185	0.2923	0.5193	0.1501	0.3532	0.0362	0.1292	-0.0611	-0.0562	-0.0201	-0.0187	0.0377	-0.0166	-0.0162	0.1288	-0.0101	-0.0487	0.1433	-0.0398	0.3099	-24.957	-94.517	-33.148
17	10.71	1.007	-0.5536	15.053	-3.058	18.9222	-0.0343	0.2396	-0.395	-0.6172	-0.0693	-0.0244	0.646	-0.4022	0.1036	0.3058	-0.0117	-0.0618	0.353	-0.0229	0.2374	-30.099	-96.303	-47.962
18	6.3303	-0.2755	1.0489	1.2665	-0.0373	0.1753	-0.0529	-0.5099	0.2825	-0.0573	0.0007	-0.0385	0.005	-0.092	0.0522	0.1621	-0.0502	-0.0334	0.1928	-0.0773	0.3283	-18.712	-92.76	-29.382
19	0.4922	0.3849	0.1636	4.0034	-0.3492	0.1389	0.0443	0.0589	0.0517	-0.1355	-0.0497	0.2368	0.0396	-0.0289	0.0053	0.1069	-0.014	-0.0757	0.1735	-0.04	0.313	-30.717	-90.891	-28.6
20	0.6181	1.5856	0.3663	12.6768	3.2733	1.0146	-0.0749	0.2802	0.0036	-0.6105	0.0055	-0.0097	-0.0688	-0.1501	0.0695	0.2145	-0.0327	-0.104	0.3089	-0.04	0.2679	-35.925	-97.031	-42.894
21	1.0396	-2.1342	-0.3268	10.1078	1.6089	0.2586	0.1282	-0.0863	-0.0346	-0.1603	-0.2323	0.7816	-0.0435	-0.0588	0.1041	0.4689	0.1042	-0.0226	0.4857	0.0846	0.5853	-44.452	-39.206	-20.884
22	2.1132	-0.9544	0.0004	2.0103	0.9945	2.1285	-0.0963	0.1298	0.0162	-0.3618	0.0782	0.2509	-0.0729	-0.1403	0.0181	0.1824	-0.0135	-0.1072	0.132	0.1015	0.3881	-31.762	-47.954	-27.406
23	12.6363	4.5978	-1.9987	3.3447	-1.9375	1.3436	-0.2492	0.5924	-0.2229	-0.3358	0.1495	0.0266	0.0208	-0.0638	0.0997	0.3501	0.0977	-0.0943	0.1363	0.1055	0.3264	-24.06	-31.13	-32.824
24	2.666	-0.3465	-1.5576	2.4056	0.4982	1.7987	0.2129	0.2476	0.204	-0.1632	-0.0989	0.0832	-0.3087	0.0232	-0.114	0.2473	0.0462	-0.0164	0.1196	0.12	0.3402	-21.533	-28.544	-28.673
25	7.1254	-4	8.1543	6.4584	-8.1491	18.5812	-0.1468	-0.3009	0.6611	0.3564	-0.0587	0.1514	-1.1033	-0.0509	0.2056	0.3335	0.062	0.0149	0.1818	0.0427	0.4823	-23.474	-17.891	-16.099
26	0.1024	0.2919	0.4279	1.2575	1.8329	2.6788	0.0519	0.0303	0.0817	-0.149	-0.1348	0.0055	-0.2197	-0.2405	0.0829	0.1915	0.1123	0.0494	0.175	0.1335	0.4606	-17.188	-49.999	-25.418
27	0.7231	1.4761	0.1521	3.4823	0.1713	0.8302	0.016	0.115	0.078	-0.0806	0.0583	-0.0713	-0.0288	-0.0748	-0.0743	0.1136	0.0758	-0.026	0.1689	0.0537	0.3341	-15.914	-67.924	-30.077
28	3.034	2.7675	-2.0031	4.5619	-3.2574	4.5962	0.0612	0.3606	0.1422	-0.0982	-0.0302	0.2191	-0.2841	0.0404	-0.031	0.1814	0.029	-0.0768	0.2101	0.0913	0.2651	-20.123	-52.048	-42.129
29	2.6868	1.5541	0.1567	3.5146	-0.4277	0.2255	0.1057	-0.0147	0.0838	0.0692	-0.2295	0.014	-0.0302	-0.0185	0.1238	0.1056	-0.0015	-0.037	0.1028	0.0065	0.2612	-16.345	-74.993	-25.047
30	2.2507	0.5838	4.3795	0.2333	1.05	8.6443	0.2456	-0.3605	-0.1934	-0.0915	0.0874	-0.0937	0.5315	-0.9788	-0.333	0.7391	-0.0573	0.2144	0.7088	0.0071	0.3618	-17.949	-71.975	-49.817
31	7.9419	-0.9995	-0.1153	3.5981	-0.2182	5.0895	0.1463	0.5415	-0.1297	-0.4217	-0.1199	0.0604	0.1556	0.1479	-0.0264	0.235	-0.0025	-0.0511	0.2547	0.06	0.1555	-14.713	-59.251	-48.653
32	0.2	0.0772	-0.0004	0.3516	0.1867	0.1769	0.015	0.1202	0.077	-0.1042	-0.0232	0.1322	-0.0662	-0.0881	0.0082	0.1324	0.0375	-0.0679	0.1208	0.0691	0.3672	-28.517	-50.967	-26.535
33	13.6504	13.5613	4.1584	18.7613	6.5419	2.4372	-0.2239	0.2033	0.9287	-1.0078	-0.1712	1.1131	-0.5381	-0.362	0.395	0.4039	0.4139	-0.0361	0.8898	0.1304	0.5319	-33.4	-20.012	-21.65
34	0.6658	-0.1677	-0.2079	1.8944	-0.1868	0.3474	0.103	0.2094	0.0789	-0.1994	-0.1876	-0.0933	-0.0556	-0.0693	0.0847	0.1485	0.0277	-0.0168	0.0935	0.0869	0.3744	-15.313	-35.655	-22.044
35	17.4144	-2.6593	6.9415	1.6206	-3.0684	6.0933	0.3031	1.6803	1.1105	0.5053	-0.9588	-0.2912	-0.8454	1.8299	0.6557	0.8121	-0.2497	-0.1811	0.5766	0.209	0.6751	-14.116	-17.553	-19.165
36	0.4537	0.9543	0.031	3.684	-0.3029	0.1437	0.0285	-0.0394	0.1038	-0.1037	-0.0712	0.1311	-0.0529	-0.0566	0.0427	0.1664	0.0538	-0.0156	0.0792	0.0407	0.3896	-23.238	-44.39	-8.536
37	1.4113	-0.1121	1.1052	1.3921	-0.2779	1.2255	0.0655	-0.0139	0.1031	0.1014	-0.1203	0.0342	-0.0487	-0.0283	0.0548	0.1151	0.0508	0.013	0.0508	0.0315	0.3496	-24.403	-46.447	-1.624
38	6.8494	-5.8614	3.4055	6.0273	-2.7159	2.637	0.0918	-0.1534	0.3366	-0.0939	-0.0086	-0.176	-0.1222	-0.1652	-0.0832	0.1649	0.0213	0.0514	0.06	0.0385	0.3719	-27.589	-43.816	-1.309
39	1.2723	1.0123	0.6107	1.8679	0.142	0.4943	-0.0144	0.0634	0.0819	-0.0457	0.0136	0.0156	-0.076	-0.0503	0.0008	0.1351	0.0666	0.0041	0.1058	0.0489	0.3649	-21.468	-46.416	-12.254
40	1.8469	2.921	2.0853	9.6761	3.5258	2.4702	0.0708	-0.0741	0.1851	0.1983	-0.175	0.4938	-0.0164	-0.2021	0.1042	0.1986	0.0958	0.0132	0.1462	0.0813	0.4025	-31.496	-32.977	-9.735
41	13.5295	-10.254	-5.7418	7.8002	4.3307	2.4647	0.2453	-0.1036	0.2278	-0.1311	-0.0136	-0.0518	-0.2142	0.0515	-0.2317	0.8521	0.101	0.343	0.573	-0.1511	0.7386	-18.709	-44.725	50.974
42	20.7605	3.5607	-4.1404	8.0158	6.7676	8.382	0.0113	0.2931	0.8024	-0.351	-0.166	0.4315	-0.3783	-0.3058	0.1546	0.3361	0.1	0.0128	0.2397	-0.0011	0.2936	-16.473	-44.767	41.989
43	0.3622	-0.2825	0.718	0.7993	-1.6014	3.2978	-0.0203	-0.0937	0.1062	0.2381	-0.0693	-0.0228	-0.45	0.0649	0.0896	0.19	0.007	0.0221	0.0905	-0.0437	0.32	-1.296	-50.628	42.965
44	8.4665	-7.3833	3.9961	11.4853	-3.7457	2.3016	0.0701	-0.0007	0.4274	0.1134	-0.0846	-0.3475	-0.255	0.1618	0.0145	0.2808	-0.0402	0.0543	0.1987	-0.0933	0.2229	0.046	-57.118	59.876
45	3.4031	-0.7683	-2.0788	1.6754	1.522	4.4838	-0.0272	-0.2543	0.2016	0.2399	0.0071	-0.0735	0.3479	0.0833	0.0201	0.216	-0.0107	-0.0167	0.1571	-0.0401	0.2317	-2.013	-61.645	60.41
46	1.6649	0.2543	-1.024	0.6096	-0.4189	1.1637	0.0751	-0.042	0.1542	0.1415	0.0359	0.0152	-0.0869	-0.0393	-0.111	0.1399	-0.0134	0.0021	0.0607	-0.0584	0.2742	-1.761	-63.532	47.404
47	2.5725	1.621	-0.848	2.4057	-2.5049	3.7095	-0.1255	-0.1159	-0.119	-0.0762	-0.0536	-0.2001	-0.0231	0.0944	0.1791	0.1131	0.0124	0.0282	0.0331	-0.0609	0.2918	11.888	-56.216	23.581
48	4.5324	-0.1426	6.158	1.2065	-0.6338	8.6947	-0.0226	-0.0909	0.0577	0.1734	0.0703	-0.0309	-0.1897	-0.0219	-0.0477	0.1997	-0.0112	0.0305	0.1549	-0.0431	0.3227	10.523	-51.651	35.901
49	3.5499	-0.2482	3.7718	2.9745	-1.9368	5.0305	0.1287	-0.0292	0.3358	0.0949	-0.3457	-0.0769	0.1093	0.2634	0.217	0.2002	0.0136	-0.0107	0.1918	-0.19	0.4321	13.784	-48.615	41.708
50	0.4221	-0.358	0.3364	1.6037	-0.6091	3.0511	-0.0077	0.0186	0.0562	-0.077	0.0177	0.046	0.1448	0.0959	-0.01	0.0841	-0.0141	0.0003	0.0653	0.0004	0.2912	9.637	-55.37	15.376
51	4.2948	-5.8331	1.6524	12.7232	-2.95	0.8206	0.4275	0.7654	0.4822	-0.278	-0.6408	-0.811	0.0474	0.4953	0.2133	0.1857	-0.1303	-0.0183	0.9977	-0.0131	0.5092	30.607	-45.097	35.288
52	3.2734	-0.5786	-0.2173	6.2579	1.0903	3.1764	0.0537	0.0265	0.2863	-0.2005	0	-0.2383	-0.1996	0.3228	-0.0538	0.1442	-0.0663	-0.0436	0.0885	-0.0576	0.3324	21.435	-48.641	37.434
53	0.2829	0.0569	0.0161	0.4697	-0.1782	0.5295	-0.0056	-0.1004	0.1247	0.1447	0.0447	0.0555	-0.14	-0.0451	-0.0391	0.1667	0.0228	0.0242	0.0901	-0.0448	0.3088	-5.683	-53.012	43.895
54	0.9482	-0.2086	-0.6273	0.2013	0.1017	3.8383	-0.0213	-0.06	0.0248	0.106	-0.0358	-0.0121	0.0217	0.1162	0.0572	0.154	-0.0117	0.007	0.1288	-0.0195	0.2716	-1.334	-68.683	50.449
55	0.1625	-2.3979	-1.7439	35.9696	26.1584	19.0333	-0.1505	-0.0727	0.0807	1.5541	1.098	-1.2293	1.1551	0.8093	-0.9474	0.966	-0.072	-0.2084	0.4787	0.0632	0.3824	-7.086	-73.903	70.31
56	0.0394	0.1104	-0.1436	0.6306	-0.2258	0.9573	0.0069	-0.0176	0.0246	0.0006	0.0213	0.0933	0.0162	-0.0781	-0.0282	0.0997	0.0103	0.0195	0.1294	-0.0072	0.3007	-17.543	-68.322	36.543
57	4.1016	-6.6859	0.0949	22.3788	-0.0831	3.6358	-0.0859	-0.2821	-0.0352	0.5541	0.0956	0.4252	0.0207	-0.414	-0.0097	0.1635	-0.0137	0.0573	0.3083	-0.0096	0.2619	-26.934	-67.108	46.57
58	1.3709	0.8148	1.7394	0.8619	0.7287	2.4553	-0.0157	0.3091	-0.0918	0.0508	0.1679	0.011	-0.0746	0.418	-0.1522	0.1073	-0.0016	0.0393	0.149	-0.0149	0.3028	-15.783	-71.908	32.67
59	0.1172	-0.1354	-0.1524	1.696	-0.9045	1.6453	0.0503	-0.056	0.0632	0.0711	-0.0072	0.1046	-0.0644	0.0198	-0.043	0.1161	0.0028	0.0202	0.1093	-0.0053	0.3096	-11.541	-64.407	38.179
60	1.1258	1.8828	-2.0191	5.5575	-4.1525	5.4659	0.0097	-0.1013	0.1797	0.1227	0.1296	0.3296	-0.1734	-0.3074	-0.1393	0.1344	0.0507	0.0448	0.2238	-0.0422	0.3006	-21.851	-62.863	50.807
61	1.4105	3.2654	1.0256	7.5612	2.3703	0.7575	0.138	0.0479	-0.2424	0.3365	0.083	-0.5392	0.0381	0.1126	-0.221	0.7322	-0.2726	0.0849	0.6601	-0.1368	0.731	9.631	-20.885	18.052
62	16.8291	4.365	-0.181	8.0162	0.3133	7.3045	-0.0125	-0.6891	0.6265	0.5562	-0.1667	-0.2414	-0.4513	0.628	0.1791	0.3558	-0.0022	-0.0318	0.1022	-0.0076	0.371	7.663	-28.561	20.594
63	0.72	0.622	-1.6294	2.6028	-1.4824	3.7285	0.0655	-0.0039	0.0864	0.2434	0.0025	0.1569	-0.1665	0.0095	-0.068	0.1978	0.0208	0.0096	0.0039	0.008	0.4587	-6.604	-30.874	13.675
64	8.3068	-0.6286	7.8731	3.2577	-0.76	13.6894	-0.1571	-0.3088	0.3132	0.0209	-0.0104	0.023	-0.4072	-0.2893	0.1675	0.2862	0.0336	0.0683	0.0167	0.0225	0.416	-7.156	-16.986	2.396
65	3.0436	1.9746	-1.0248	2.2859	-0.5045	1.5214	0.0688	-0.0116	0.3742	0.0283	0.0679	0.1822	-0.2548	-0.1015	-0.1367	0.2579	0.0203	-0.0206	0.0217	0.0389	0.5351	-3.599	-17.544	-1.619
66	3.2194	3.1969	-2.0337	9.4501	-5.3717	3.8573	-0.0702	-0.0393	0.093	-0.3331	-0.1505	-0.3776	0.0223	0.2953	0.2206	0.2493	-0.0278	-0.0063	0.0599	0.0097	0.3777	6.11	-22.77	-5.153
67	0.982	0.1082	-0.0381	0.6791	-0.9768	2.1162	-0.0176	-0.0115	0.107	-0.049	0.0352	0.0695	0.0061	-0.0774	-0.0177	0.1023	0.0164	0.0038	0.0142	-0.0036	0.3446	-15.601	-49.992	13.811
68	4.4454	-2.5518	2.4614	2.9419	-2.165	4.0181	0.0339	0.0799	0.387	-0.0364	-0.1657	-0.1038	-0.3658	-0.147	0.1318	0.2154	0.0693	0.02	0.0454	-0.0273	0.383	-21.149	-32.102	14.258
69	0.6966	-0.6968	1.0449	1.5407	0.04	3.3968	-0.0021	-0.0346	0.0624	-0.0312	0.0608	0.0285	-0.1282	0.0989	-0.0586	0.0809	-0.0099	0.0188	0.0756	-0.0066	0.3289	-14.55	-58.167	19.433
70	4.763	1.8102	-0.8341	5.178	-3.3101	25.4943	0.0756	-0.1975	-0.1676	0.3203	-0.0584	0.4219	0.3214	-0.2851	-0.0172	0.2193	0.1062	0.0255	0.2947	-0.0236	0.508	-36.843	-38.558	18.687
71	3.5975	0.7191	-1.4539	5.0546	2.1795	4.8002	0.0638	-0.2991	0.0736	0.1648	-0.1398	0.2159	-0.1173	-0.3295	0.0761	0.1457	0.087	0.0155	0.1221	-0.0112	0.3573	-28.007	-36.189	15.801
72	0.5654	-0.602	0.6359	0.7528	-0.6293	1.3438	0.0071	0.0079	0.0879	0.0883	-0.0262	-0.0264	-0.1258	0.1019	0.0191	0.1807	-0.0212	0.0144	0.0439	-0.0166	0.3389	0.55	-38.528	17.361
73	3.2527	0.2423	-0.7104	5.0238	-5.5645	10.9261	-0.0437	-0.1368	0.3489	0.4141	-0.0554	-0.233	-0.683	0.079	0.0992	0.2468	-0.0179	-0.0039	0.0166	0.0028	0.4489	7.51	-15.433	3.073
74	0.9371	-0.3134	0.2998	4.4984	-0.2927	0.6776	-0.0069	0.0768	0.1226	-0.2894	-0.0169	0.1131	-0.1486	-0.0777	0.0238	0.1789	0.0125	-0.0009	0.0345	0.0655	0.3837	-3.494	-27.465	-6.367
75	0.5006	0.5416	-1.7287	1.5782	-2.6266	6.6384	0.0967	-0.014	-0.0044	-0.0571	-0.0002	0.0414	-0.3553	0.0301	-0.0964	0.2927	-0.038	-0.0068	0.0333	0.0875	0.3989	7.286	-25.812	-10.726
76	0.456	-0.4319	0.0857	0.4215	0.0085	1.4059	0.0066	0.0124	0.0853	-0.0102	-0.0207	-0.0399	-0.0565	0.078	0.0141	0.102	-0.0294	0.0004	0.0585	0.0109	0.3736	15.916	-44.061	3.529
77	13.3518	4.4575	4.6698	15.2022	4.9091	11.8124	0.1717	0.462	0.9138	-0.5806	-0.299	-0.2948	-0.7721	0.4823	0.1273	0.2348	-0.0724	-0.0004	0.0837	0.0367	0.4751	23.157	-27.351	2.786
78	1.4941	-2.2977	-1.095	4.3663	1.103	1.2079	-0.0165	0.0283	-0.2001	0.0993	-0.1197	0.3335	-0.0312	0.0374	0.1363	0.1222	-0.0531	0.0042	0.0587	0.0679	0.3795	13.902	-46.027	0.608
79	0.1258	-0.0032	-0.4374	0.562	-0.9472	3.5024	0.0065	-0.0083	0.1109	0.0063	0.0427	-0.0512	-0.2002	-0.0114	-0.0491	0.1619	-0.0356	-0.0174	0.0394	0.0392	0.4188	6.569	-38.626	2.944
80	1.9129	1.2713	-3.8964	3.5366	-4.3175	9.0959	0.1239	-0.2654	0.1768	0.1547	-0.1233	-0.2156	-0.3121	0.5309	-0.0005	0.2118	-0.0698	-0.027	0.0603	0.0288	0.47	15.92	-25.073	2.047

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	36 - 48
2	X-RAY DIFFRACTION	2	A	49 - 64
3	X-RAY DIFFRACTION	3	A	65 - 91
4	X-RAY DIFFRACTION	4	A	92 - 113
5	X-RAY DIFFRACTION	5	A	114 - 124
6	X-RAY DIFFRACTION	6	A	125 - 143
7	X-RAY DIFFRACTION	7	A	144 - 173
8	X-RAY DIFFRACTION	8	A	174 - 203
9	X-RAY DIFFRACTION	9	A	204 - 221
10	X-RAY DIFFRACTION	10	A	222 - 249
11	X-RAY DIFFRACTION	11	A	250 - 274
12	X-RAY DIFFRACTION	12	A	275 - 309
13	X-RAY DIFFRACTION	13	A	310 - 327
14	X-RAY DIFFRACTION	14	A	328 - 364
15	X-RAY DIFFRACTION	15	A	365 - 371
16	X-RAY DIFFRACTION	16	A	372 - 431
17	X-RAY DIFFRACTION	17	A	432 - 440
18	X-RAY DIFFRACTION	18	A	441 - 455
19	X-RAY DIFFRACTION	19	A	456 - 487
20	X-RAY DIFFRACTION	20	A	488 - 512
21	X-RAY DIFFRACTION	21	B	36 - 48
22	X-RAY DIFFRACTION	22	B	49 - 74
23	X-RAY DIFFRACTION	23	B	75 - 91
24	X-RAY DIFFRACTION	24	B	92 - 116
25	X-RAY DIFFRACTION	25	B	117 - 125
26	X-RAY DIFFRACTION	26	B	126 - 144
27	X-RAY DIFFRACTION	27	B	145 - 171
28	X-RAY DIFFRACTION	28	B	172 - 201
29	X-RAY DIFFRACTION	29	B	202 - 229
30	X-RAY DIFFRACTION	30	B	230 - 243
31	X-RAY DIFFRACTION	31	B	244 - 268
32	X-RAY DIFFRACTION	32	B	269 - 320
33	X-RAY DIFFRACTION	33	B	321 - 328
34	X-RAY DIFFRACTION	34	B	329 - 364
35	X-RAY DIFFRACTION	35	B	365 - 373
36	X-RAY DIFFRACTION	36	B	374 - 395
37	X-RAY DIFFRACTION	37	B	396 - 430
38	X-RAY DIFFRACTION	38	B	431 - 451
39	X-RAY DIFFRACTION	39	B	452 - 487
40	X-RAY DIFFRACTION	40	B	488 - 512
41	X-RAY DIFFRACTION	41	C	36 - 46
42	X-RAY DIFFRACTION	42	C	48 - 55
43	X-RAY DIFFRACTION	43	C	56 - 74
44	X-RAY DIFFRACTION	44	C	75 - 91
45	X-RAY DIFFRACTION	45	C	92 - 115
46	X-RAY DIFFRACTION	46	C	116 - 146
47	X-RAY DIFFRACTION	47	C	147 - 167
48	X-RAY DIFFRACTION	48	C	168 - 183
49	X-RAY DIFFRACTION	49	C	184 - 203
50	X-RAY DIFFRACTION	50	C	204 - 232
51	X-RAY DIFFRACTION	51	C	233 - 249
52	X-RAY DIFFRACTION	52	C	250 - 269
53	X-RAY DIFFRACTION	53	C	270 - 330
54	X-RAY DIFFRACTION	54	C	331 - 364
55	X-RAY DIFFRACTION	55	C	365 - 371
56	X-RAY DIFFRACTION	56	C	372 - 422
57	X-RAY DIFFRACTION	57	C	423 - 440
58	X-RAY DIFFRACTION	58	C	441 - 459
59	X-RAY DIFFRACTION	59	C	460 - 487
60	X-RAY DIFFRACTION	60	C	488 - 512
61	X-RAY DIFFRACTION	61	D	38 - 44
62	X-RAY DIFFRACTION	62	D	45 - 58
63	X-RAY DIFFRACTION	63	D	59 - 73
64	X-RAY DIFFRACTION	64	D	74 - 92
65	X-RAY DIFFRACTION	65	D	93 - 118
66	X-RAY DIFFRACTION	66	D	119 - 134
67	X-RAY DIFFRACTION	67	D	135 - 171
68	X-RAY DIFFRACTION	68	D	172 - 201
69	X-RAY DIFFRACTION	69	D	202 - 234
70	X-RAY DIFFRACTION	70	D	235 - 250
71	X-RAY DIFFRACTION	71	D	251 - 276
72	X-RAY DIFFRACTION	72	D	277 - 310
73	X-RAY DIFFRACTION	73	D	311 - 331
74	X-RAY DIFFRACTION	74	D	332 - 369
75	X-RAY DIFFRACTION	75	D	370 - 385
76	X-RAY DIFFRACTION	76	D	386 - 430
77	X-RAY DIFFRACTION	77	D	431 - 439
78	X-RAY DIFFRACTION	78	D	440 - 456
79	X-RAY DIFFRACTION	79	D	457 - 487
80	X-RAY DIFFRACTION	80	D	488 - 512

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

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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

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Covid-19 info

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