PDB-3mol: Structure of dimeric holo HasAp H32A Mutant from Pseudomonas aeru...

ID or keywords:

Entry

Database: PDB / ID: 3mol

Title

Structure of dimeric holo HasAp H32A Mutant from Pseudomonas aeruginosa to 1.20A Resolution

Components

Heme acquisition protein HasAp

Keywords

HEME BINDING PROTEIN / TRANSPORT PROTEIN / hemophore / heme transport / H32A mutation / holo protein

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.2 Å

Authors

Lovell, S. / Battaile, K.P. / Jepkorir, G. / Rodriguez, J.C. / Rui, H. / Im, W. / Alontaga, A.Y. / Yukl, E. / Moenne-Loccoz, P. / Rivera, M.

Citation

Journal: J.Am.Chem.Soc. / Year: 2010
Title: Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa.
Authors: Jepkorir, G. / Rodriguez, J.C. / Rui, H. / Im, W. / Lovell, S. / Battaile, K.P. / Alontaga, A.Y. / Yukl, E.T. / Rivera, M.

History

Deposition	Apr 22, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 28, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 17, 2019	Group: Data collection / Derived calculations / Refinement description Category: pdbx_struct_special_symmetry / software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.3	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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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	3mol.cif.gz	155.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3mol.ent.gz	123.6 KB	Display	PDB format
PDBx/mmJSON format	3mol.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3mol_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3mol_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3mol_validation.xml.gz	19.5 KB	Display
Data in CIF	3mol_validation.cif.gz	28.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/3mol ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3mol	HTTPS FTP

-
Related structure data

Related structure data	3mokSC 3momC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4f27-d 3uwo-d 3mwk-d 6urb-d 3mwl-d 5xal-d 2gxq-1 3roh-d 4gpv-2 2p0o-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

Deposited unit

A: Heme acquisition protein HasAp

B: Heme acquisition protein HasAp

hetero molecules

38.9 kDa, 2 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)	71.740, 52.700, 85.714
Angle α, β, γ (deg.)	90.000, 91.480, 90.000
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	A-317- HOH

#1: Protein	Heme acquisition protein HasAp Mass: 18834.467 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-184 / Mutation: H32A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: hasAp, PA14_20020 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: Q02QP5, UniProt: G3XD33*PLUS
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.15 Å³/Da / Density % sol: 42.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.26 M ammonium sulfate, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.2→30 Å / Num. obs: 95175 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / B_iso Wilson estimate: 19.211 Å² / R_merge(I) obs: 0.041 / Net I/σ(I): 16.96
Reflection shell	Resolution: 1.2→1.3 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 68621 / Num. unique all: 19526 / Num. unique obs: 19526 / % possible all: 91.9

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	1.57 Å	19.25 Å
Translation	1.57 Å	19.25 Å

-
Processing

Software

Name	Version	Classification
PHENIX	1.6_289	refinement
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MOK

3mok

Resolution: 1.2→19.245 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.16 / σ(F): 0.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.197	4379	5.01 %	RANDOM
R_work	0.177	-	-	-
obs	0.178	87374	87.56 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.396 Å² / k_sol: 0.466 e/Å³

Displacement parameters

B_iso max: 61.66 Å² / B_iso mean: 21.543 Å² / B_iso min: 7.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.825 Å²	0 Å²	-0.275 Å²
2-	-	6.513 Å²	0 Å²
3-	-	-	-2.688 Å²

Refinement step

Cycle: LAST / Resolution: 1.2→19.245 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2588	0	86	305	2979

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_bond_d	0.01
X-RAY DIFFRACTION	f_angle_deg	1.421

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.2-1.243	0.256	329	0.247	6879	7208	73
1.243-1.293	0.255	360	0.221	7227	7587	76
1.293-1.352	0.233	430	0.211	7843	8273	83
1.352-1.423	0.23	412	0.196	7870	8282	83
1.423-1.512	0.208	450	0.183	8301	8751	88
1.512-1.628	0.199	441	0.172	8648	9089	91
1.628-1.792	0.212	475	0.168	8742	9217	92
1.792-2.051	0.199	486	0.169	8929	9415	94
2.051-2.583	0.183	500	0.167	9211	9711	97
2.583-19.247	0.178	496	0.17	9345	9841	97

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	0.1293	0.2015	0.0532	0.2435	0.041	0.028	0.181	0.0315	-0.0822	0.0311	-0.064	0.2153	0.159	-0.0756	0.0001	0.1474	-0.0136	-0.0013	0.1249	0.0247	0.1497	-26.5745	-6.1204	36.085
2	0.2114	0.0669	0.0992	0.034	-0.0337	0.253	-0.0849	-0.2083	0.1311	0.2113	0.1469	-0.0816	0.0738	-0.0951	0.0041	0.1487	0.0205	-0.0087	0.1112	-0.0249	0.1377	-20.3763	0.7447	41.1079
3	0.0586	-0.1083	-0.0164	0.1367	0.0598	0.0735	0.0101	-0.129	-0.0039	0.0878	-0.0628	0.0301	-0.049	-0.0353	-0.0001	0.1373	0.0037	-0.0034	0.0938	-0.0102	0.1126	-8.9199	-1.2062	43.182
4	0.1757	-0.0548	0.0859	0.2831	-0.1523	0.0878	-0.1554	0.1098	-0.2732	0.1537	0.0255	0.039	0.3733	0.006	-0	0.1909	0.0016	-0.0123	0.1167	-0.0179	0.1607	-5.7737	-10.1612	42.7808
5	0.4097	0.0197	-0.2864	0.4031	0.1263	0.218	0.0826	-0.0505	-0.1071	-0.0475	-0.1249	-0.2993	0.2118	0.2794	-0.0003	0.1523	0.0188	0.0094	0.1313	-0.0073	0.1474	-5.3388	-6.4646	20.2501
6	0.1131	0.009	-0.1163	0.1808	0.1691	0.2163	0.0439	0.0038	-0.0896	0.0217	0.0203	-0.0375	0.0371	0.0435	0.0003	0.1175	0.0089	-0.0157	0.071	-0.0121	0.1083	-9.4087	-4.6507	29.0984
7	0.0435	0.0496	-0.0936	0.0551	-0.0747	0.191	-0.1321	0.1144	-0.2393	-0.2634	-0.0141	-0.1074	0.1458	-0.0036	-0.0001	0.1305	0.005	0.0211	0.1553	0.0261	0.1219	-6.5853	3.3128	14.8159
8	0.0828	-0.0735	-0.0031	0.1388	0.1061	0.1242	-0.2165	0.4221	0.075	-0.3622	0.0305	0.0499	0.122	0.2315	0.0004	0.156	-0.0126	-0.0055	0.1723	0.0557	0.1398	-6.553	9.0653	15.4705
9	0.0451	-0.0144	-0.0644	0.0236	-0.0387	0.1779	-0.017	0.2705	-0.0887	-0.1294	0.016	0.1583	0.2501	-0.3041	-0.0032	0.1331	0.0204	-0.0033	0.0939	0.0078	0.1084	-17.7054	1.1258	17.1067
10	0.0122	-0.0417	-0.0398	0.2218	0.1209	0.0849	-0.0095	-0.0812	0.0156	0.0953	0.0817	-0.0591	-0.0349	0.0241	0	0.1369	0.0066	-0.0189	0.0806	-0.0075	0.1349	-14.1294	-6.7233	32.112
11	0.1583	-0.0102	0.0864	0.1348	-0.0529	0.1049	-0.0655	-0.0505	-0.1196	0.0289	0.16	-0.1837	0.2615	0.2097	0.0112	0.1778	-0.0027	-0.0247	0.0937	-0.047	0.1891	-10.0534	-14.272	25.1085
12	0.072	0.062	-0.013	0.085	0.0253	0.1104	0.1056	-0.1001	-0.0068	0.1095	0.0677	-0.3648	0.2889	0.021	-0.0003	0.1599	0.0022	-0.0282	0.0838	-0.005	0.1568	-17.0905	-10.0778	36.1091
13	0.3606	-0.0459	-0.0271	0.2012	0.1457	0.1112	0.0812	0.3512	0.0987	-0.1683	0.0538	0.1043	0.0054	-0.1578	-0.0002	0.1438	0.0119	-0.0096	0.1502	0.0314	0.1681	-24.0301	-0.7293	24.0748
14	0.0515	0.033	-0.0982	0.0612	-0.0503	0.1447	0.0723	-0.1043	0.274	0.1296	0.0225	-0.0255	-0.2435	-0.2039	-0	0.1614	0.0093	-0.0106	0.1343	0.0311	0.1544	-14.1816	11.2169	15.8606
15	0.0804	-0.0112	-0.107	0.0486	-0.0637	0.1898	-0.0027	0.1161	0.2	0.0351	0.0051	-0.0034	-0.1912	0.0922	0.0001	0.1438	0.0079	-0.0035	0.0823	0.0189	0.1312	-13.5836	7.67	24.0016
16	0.4178	-0.0084	0.0831	0.4031	-0.3888	0.4738	0.0289	0.0576	0.1732	0.0646	0.0209	0.0457	-0.0516	-0.0214	-0.0003	0.1592	0.025	-0.0011	0.0778	0.0029	0.1486	-19.0445	6.1839	31.2405
17	0.049	-0.0197	0.0169	0.0133	0.0003	0.006	-0.0882	-0.2817	0.6864	0.1295	0.1205	0.1331	-0.4992	-0.485	-0.0004	0.1607	0.093	0.0145	0.2922	0.0183	0.2343	-35.8424	6.8152	31.3648
18	0.0711	0.0505	-0.0012	0.0734	0.068	0.0842	0.0846	0.0258	0.1867	-0.0257	0.0456	0.13	-0.067	-0.3468	-0.0002	0.1602	0.0347	0.0121	0.1668	0.0134	0.1791	-29.7775	3.2743	38.4472
19	0.0719	0.0953	-0.0543	0.1331	-0.0861	0.0511	0.0496	-0.0023	0.1309	0.0715	-0.0962	0.2206	-0.2713	-0.3454	-0.0001	0.1352	-0.0151	0.0247	0.2071	0.0231	0.1904	-34.4314	-3.0838	36.8778
20	0.1117	0.0542	-0.1157	0.0945	-0.0388	0.1015	0.508	0.1843	-0.0748	0.1367	-0.442	-0.2352	0.2951	0.3476	0.0009	0.2065	-0.0259	-0.0313	0.1701	0.0351	0.1969	-25.4342	-11.7465	36.9086
21	0.0578	0.0758	-0.0086	0.061	-0.0161	0.0048	-0.2184	0.9475	-0.4006	-0.144	0.1121	-0.2317	0.2594	-0.0464	-0.0001	0.1978	-0.0413	0.0613	0.5193	-0.0368	0.272	26.7884	-5.1955	11.4836
22	0.009	0.0223	-0.0019	0.0165	0.0036	-0.0011	0.0913	0.808	-0.2486	0.0787	-0.494	-0.2161	0.4548	-0.0269	0.0026	0.202	-0.1024	0.0644	0.9722	-0.0003	0.2131	25.4969	0.4786	1.3153
23	0.0389	0.0176	0.0825	0.0323	0.0627	0.1333	-0.167	0.8353	0.0526	-0.087	0.0067	-0.0761	-0.025	-0.3963	-0.0002	0.1363	-0.0789	0.0152	0.7408	0.1308	0.169	17.052	6.1659	6.3805
24	0.0312	0.0376	-0.0266	0.0506	-0.0093	0.0385	-0.2719	0.0699	0.3398	-0.054	0.1025	-0.0946	0.2153	-0.4613	0.0006	0.2024	-0.0674	-0.0069	0.7377	0.0989	0.1885	10.6103	7.0943	-2.0203
25	0.0364	-0.0103	0.0451	-0.0014	-0.0221	0.0407	0.4085	0.0248	-0.0644	0.2723	-0.0854	0.2072	0.0687	0.211	-0.0013	0.3681	-0.1181	0.0939	0.8189	0.0813	0.3759	3.6323	0.1998	0.8334
26	0.1101	-0.0287	-0.0311	0.0926	-0.015	0.1201	-0.3567	1.064	-0.4163	-0.1183	-0.1318	0.0457	0.2908	-0.4021	-0.0024	0.1963	-0.1015	0.09	0.4398	-0.1545	0.2367	4.4687	-6.4348	19.4651
27	0.7707	-0.4227	0.4498	0.7041	-0.2408	0.4765	-0.4972	0.3622	-0.4739	0.0856	0.0342	0.1458	0.1486	-0.1409	-0.0517	0.1438	-0.0549	0.0516	0.1661	-0.073	0.1685	5.5569	-6.3323	25.1017
28	0.0679	-0.0239	0.0319	0.047	-0.1131	0.1346	-0.3769	0.8026	0.1306	0.0241	0.4221	0.0313	0.0811	-0.3752	0.001	0.1466	-0.0998	0.0186	0.5091	0.0195	0.1427	6.3942	-0.0996	13.8297
29	0.0786	0.0015	-0.0569	0.0602	-0.0639	0.0593	-0.173	1.0479	0.1292	0.0644	0.1585	0.2002	-0.2754	-0.5424	-0.0013	0.1523	-0.0552	0.0198	0.6754	0.0478	0.1809	8.0522	1.2965	8.6928
30	0.4233	0.283	-0.2567	0.2877	-0.0864	0.1284	-0.1199	0.1579	0.1386	0.1561	-0.0511	-0.082	-0.1547	0.0642	-0.0091	0.1409	-0.0089	-0.0118	0.1034	0.0162	0.1177	6.5387	2.125	30.1604
31	0.3937	-0.3507	0.2649	1.4263	-0.7388	0.5004	-0.2273	0.4247	-0.0327	0.0826	-0.0909	-0.2447	0.028	0.0325	-0.1171	0.1365	-0.0352	0.0303	0.1907	0.0239	0.1619	15.6817	-2.113	25.041
32	0.1026	0.0926	0.0334	0.0966	0.0372	0.0118	-0.4926	1.263	-0.1211	-0.2045	0.0868	0.2906	0.682	-0.3932	0.0017	0.2823	-0.2471	0.118	0.6645	-0.1615	0.2728	9.2856	-6.4398	10.2355
33	0.0105	0.0065	-0.0243	0.002	-0.0084	0.0313	-0.3062	0.3779	0.1141	0.0647	-0.2684	0.1531	0.5078	0.0597	0.0008	0.2196	-0.1636	0.0877	0.7303	-0.1244	0.2483	15.3269	-5.5882	6.007
34	0.0985	0.0042	0.0283	0.0704	0.0418	0.0499	-0.3892	0.266	-0.2069	0.171	0.0114	-0.0094	0.5402	0.1657	0.0006	0.1745	-0.0073	0.0532	0.3271	0.0291	0.206	22.6395	-3.1002	20.8436
35	0.0623	-0.0052	-0.0839	0.0273	-0.044	0.1219	-0.136	0.062	0.4664	0.4311	-0.1094	-0.3313	-0.321	0.3878	-0.0001	0.2006	-0.0464	-0.0516	0.1568	0.0435	0.2089	13.6657	5.9163	32.7274
36	0.0978	0.0055	-0.0765	0.0663	-0.0845	0.1492	0.1075	0.2589	0.4301	0.1785	-0.155	-0.1224	-0.3659	0.0848	0.0002	0.1636	-0.0268	0.0039	0.2036	0.0881	0.2086	14.1971	6.9802	24.3357
37	0.1464	0.0526	-0.1755	0.2026	0.1588	0.446	-0.125	0.4429	0.2559	0.1123	0.0871	-0.0583	-0.1786	-0.1319	-0.0005	0.1541	-0.0197	0.0113	0.3778	0.1103	0.2002	20.5246	6.3026	16.7785
38	0.0399	0.0255	-0.0103	0.0105	-0.0145	0.0297	-0.1411	-0.198	0.06	0.3328	-0.1389	-0.1986	-0.1945	0.0572	0.0004	0.1595	-0.0383	-0.0181	0.3552	0.0891	0.2699	36.8802	3.13	17.3672
39	0.0405	-0.0483	0.0245	0.0957	-0.0794	0.0639	-0.2057	0.9551	0.1199	0.1196	0.0514	-0.1858	-0.1298	0.3132	-0.0013	0.1398	-0.0864	0.0256	0.5765	0.0312	0.1967	30.9132	3.3909	7.9932
40	0.0336	-0.0354	-0.0057	0.0417	0.0324	0.0359	-0.0967	0.3137	-0.398	-0.0212	0.0102	-0.209	0.4726	0.2754	0.0001	0.1821	-0.0121	0.0995	0.5558	-0.085	0.3277	32.8879	-4.7636	9.4646

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 2:12)	A	2 - 12
2	X-RAY DIFFRACTION	2	(chain A and resid 13:23)	A	13 - 23
3	X-RAY DIFFRACTION	3	(chain A and resid 24:33)	A	24 - 33
4	X-RAY DIFFRACTION	4	(chain A and resid 34:41)	A	34 - 41
5	X-RAY DIFFRACTION	5	(chain A and resid 42:52)	A	42 - 52
6	X-RAY DIFFRACTION	6	(chain A and resid 53:71)	A	53 - 71
7	X-RAY DIFFRACTION	7	(chain A and resid 72:79)	A	72 - 79
8	X-RAY DIFFRACTION	8	(chain A and resid 80:85)	A	80 - 85
9	X-RAY DIFFRACTION	9	(chain A and resid 86:90)	A	86 - 90
10	X-RAY DIFFRACTION	10	(chain A and resid 91:98)	A	91 - 98
11	X-RAY DIFFRACTION	11	(chain A and resid 99:109)	A	99 - 109
12	X-RAY DIFFRACTION	12	(chain A and resid 110:114)	A	110 - 114
13	X-RAY DIFFRACTION	13	(chain A and resid 115:122)	A	115 - 122
14	X-RAY DIFFRACTION	14	(chain A and resid 123:130)	A	123 - 130
15	X-RAY DIFFRACTION	15	(chain A and resid 131:138)	A	131 - 138
16	X-RAY DIFFRACTION	16	(chain A and resid 139:156)	A	139 - 156
17	X-RAY DIFFRACTION	17	(chain A and resid 157:162)	A	157 - 162
18	X-RAY DIFFRACTION	18	(chain A and resid 163:169)	A	163 - 169
19	X-RAY DIFFRACTION	19	(chain A and resid 170:177)	A	170 - 177
20	X-RAY DIFFRACTION	20	(chain A and resid 178:184)	A	178 - 184
21	X-RAY DIFFRACTION	21	(chain B and resid 2:8)	B	2 - 8
22	X-RAY DIFFRACTION	22	(chain B and resid 9:15)	B	9 - 15
23	X-RAY DIFFRACTION	23	(chain B and resid 16:28)	B	16 - 28
24	X-RAY DIFFRACTION	24	(chain B and resid 29:35)	B	29 - 35
25	X-RAY DIFFRACTION	25	(chain B and resid 36:42)	B	36 - 42
26	X-RAY DIFFRACTION	26	(chain B and resid 43:48)	B	43 - 48
27	X-RAY DIFFRACTION	27	(chain B and resid 49:55)	B	49 - 55
28	X-RAY DIFFRACTION	28	(chain B and resid 56:60)	B	56 - 60
29	X-RAY DIFFRACTION	29	(chain B and resid 61:68)	B	61 - 68
30	X-RAY DIFFRACTION	30	(chain B and resid 69:84)	B	69 - 84
31	X-RAY DIFFRACTION	31	(chain B and resid 85:92)	B	85 - 92
32	X-RAY DIFFRACTION	32	(chain B and resid 93:108)	B	93 - 108
33	X-RAY DIFFRACTION	33	(chain B and resid 109:114)	B	109 - 114
34	X-RAY DIFFRACTION	34	(chain B and resid 115:122)	B	115 - 122
35	X-RAY DIFFRACTION	35	(chain B and resid 123:129)	B	123 - 129
36	X-RAY DIFFRACTION	36	(chain B and resid 130:138)	B	130 - 138
37	X-RAY DIFFRACTION	37	(chain B and resid 139:156)	B	139 - 156
38	X-RAY DIFFRACTION	38	(chain B and resid 157:163)	B	157 - 163
39	X-RAY DIFFRACTION	39	(chain B and resid 164:170)	B	164 - 170
40	X-RAY DIFFRACTION	40	(chain B and resid 171:180)	B	171 - 180

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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