PDB-4cpi: streptavidin A86D mutant with love-hate ligand 4

ID or keywords:

Entry

Database: PDB / ID: 4cpi

Title

streptavidin A86D mutant with love-hate ligand 4

Components

STREPTAVIDIN

Keywords

BIOTIN BINDING PROTEIN /

AVIDIN /

BIOTIN / STRAIN / BIOTINYLATED /

STERIC CLASH / STRAINED /

HINDERED /

FORCE / LIGAND SERIES / AFFINITY

Function / homology

Function and homology information

biotin binding / extracellular region
Similarity search - Function

Biological species

STREPTOMYCES AVIDINII (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.54 Å

Authors

Fairhead, M. / Shen, D. / Chan, L.K.M. / Lowe, E.D. / Donohoe, T.J. / Howarth, M.

Citation

Journal: Bioorg.Med.Chem. / Year: 2014
Title: Love-Hate Ligands for High Resolution Analysis of Strain in Ultra-Stable Protein/Small Molecule Interaction.
Authors: Fairhead, M. / Shen, D. / Chan, L.K.M. / Lowe, E.D. / Donohoe, T.J. / Howarth, M.

History

Deposition	Feb 6, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 6, 2014	Provider: repository / Type: Initial release
Revision 1.1	Aug 27, 2014	Group: Database references
Revision 1.2	Oct 1, 2014	Group: Database references
Revision 1.3	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4cpi.cif.gz	219.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4cpi.ent.gz	177.9 KB	Display	PDB format
PDBx/mmJSON format	4cpi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cp/4cpi ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cpi	HTTPS FTP

-
Related structure data

Related structure data	4cpeC 4cpfC 4cphC 3ry1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4cpf-1 6m9b-d 1swp-d 4bx5-d 6vjl-1 7kbz-d 1lcw-1 2rtc-1 5n8j-d 1df8-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: STREPTAVIDIN

B: STREPTAVIDIN

C: STREPTAVIDIN

D: STREPTAVIDIN

hetero molecules

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

1

D: STREPTAVIDIN

hetero molecules

D: STREPTAVIDIN

hetero molecules

C: STREPTAVIDIN

hetero molecules

C: STREPTAVIDIN

hetero molecules

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

2

A: STREPTAVIDIN

B: STREPTAVIDIN

hetero molecules

A: STREPTAVIDIN

B: STREPTAVIDIN

hetero molecules

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

3

C: STREPTAVIDIN

hetero molecules

C: STREPTAVIDIN

hetero molecules

D: STREPTAVIDIN

hetero molecules

D: STREPTAVIDIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.260, 81.250, 90.690
Angle α, β, γ (deg.)	90.00, 103.84, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-2029- HOH
2	1	D-2030- HOH

#1: Protein	STREPTAVIDIN / Mass: 13325.346 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-163 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#2: Chemical	ChemComp-LH4 / 5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4- d]imidazolidin-4-yl]-N'-{2,6-bis[4-(morpholine-4- sulfonyl)phenyl]phenyl}pentanehydrazide Mass: 784.965 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₆H₄₄N₆O₈S₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	N-TERMINAL METHIONINE REMOVED IN MATURE PROTEIN, ALANINE 86 ASPARTATE MUTATION

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	Method: vapor diffusion, sitting drop / pH: 8.5 Details: CONDITION A9 OF THE MORPHEUS SCREEN: 0.1 M BICINE/TRIZMA BASE PH 8.5, 10% W/V POLYETHYLENE GLYCOL 20,000, 20% V/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 30 MM MAGNESIUM CHLORIDE AND 30 MM ...Details: CONDITION A9 OF THE MORPHEUS SCREEN: 0.1 M BICINE/TRIZMA BASE PH 8.5, 10% W/V POLYETHYLENE GLYCOL 20,000, 20% V/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 30 MM MAGNESIUM CHLORIDE AND 30 MM CALCIUM CHLORIDE. SITTING DROP.

Crystal

Density Matthews: 2.7 Å³/Da / Density % sol: 54 % / Description: NONE

Crystal grow

Method: vapor diffusion, sitting drop / pH: 8.5
Details: CONDITION A9 OF THE MORPHEUS SCREEN: 0.1 M BICINE/TRIZMA BASE PH 8.5, 10% W/V POLYETHYLENE GLYCOL 20,000, 20% V/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 30 MM MAGNESIUM CHLORIDE AND 30 MM ...

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.54→39.45 Å / Num. obs: 84164 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / B_iso Wilson estimate: 17.55 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.54→1.6 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 2.34 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
xia2		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RY1

3ry1

Resolution: 1.54→39.45 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.95 / Stereochemistry target values: ML
Details: RESIDUES 46-48 ARE MODELLED STEREOCHEMICALLY DUE TO POOR DENSITY IN CHAINS A AND D. 46-48 ARE OMITTED FROM CHAINS B AND C. LH4 B1000 AND C1000 REPRESENT LH4 SHOWN WITHOUT THE AROMATIC ...

	R_factor	Num. reflection	% reflection
R_free	0.1815	4202	5 %
R_work	0.1571	-	-
obs	0.1583	84162	99.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.54→39.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3568	0	170	311	4049

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4166
X-RAY DIFFRACTION	f_angle_d	1.169	5725
X-RAY DIFFRACTION	f_dihedral_angle_d	12.435	1468
X-RAY DIFFRACTION	f_chiral_restr	0.048	621
X-RAY DIFFRACTION	f_plane_restr	0.006	765

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.54-1.5575	0.3007	130	0.2613	2681	X-RAY DIFFRACTION	100
1.5575-1.5758	0.2696	138	0.2521	2607	X-RAY DIFFRACTION	99
1.5758-1.595	0.2773	165	0.2385	2698	X-RAY DIFFRACTION	100
1.595-1.6152	0.2652	137	0.2343	2584	X-RAY DIFFRACTION	100
1.6152-1.6365	0.2282	121	0.2184	2719	X-RAY DIFFRACTION	100
1.6365-1.6589	0.2098	137	0.2065	2665	X-RAY DIFFRACTION	100
1.6589-1.6826	0.2311	140	0.1964	2661	X-RAY DIFFRACTION	100
1.6826-1.7077	0.2461	144	0.1886	2628	X-RAY DIFFRACTION	100
1.7077-1.7344	0.1979	147	0.1795	2719	X-RAY DIFFRACTION	100
1.7344-1.7628	0.19	121	0.1659	2645	X-RAY DIFFRACTION	100
1.7628-1.7932	0.206	119	0.1632	2673	X-RAY DIFFRACTION	100
1.7932-1.8258	0.177	150	0.1584	2640	X-RAY DIFFRACTION	100
1.8258-1.861	0.1637	157	0.1518	2674	X-RAY DIFFRACTION	100
1.861-1.899	0.1866	113	0.1556	2681	X-RAY DIFFRACTION	100
1.899-1.9402	0.2028	130	0.1546	2669	X-RAY DIFFRACTION	100
1.9402-1.9854	0.1723	151	0.1466	2659	X-RAY DIFFRACTION	100
1.9854-2.035	0.1545	157	0.1459	2644	X-RAY DIFFRACTION	100
2.035-2.09	0.1753	120	0.1462	2667	X-RAY DIFFRACTION	100
2.09-2.1515	0.1647	173	0.1473	2630	X-RAY DIFFRACTION	100
2.1515-2.221	0.1772	146	0.1443	2683	X-RAY DIFFRACTION	100
2.221-2.3004	0.1669	133	0.15	2689	X-RAY DIFFRACTION	100
2.3004-2.3924	0.1795	153	0.1588	2661	X-RAY DIFFRACTION	100
2.3924-2.5013	0.1817	136	0.159	2648	X-RAY DIFFRACTION	100
2.5013-2.6332	0.1891	135	0.1559	2678	X-RAY DIFFRACTION	100
2.6332-2.7981	0.1845	136	0.1514	2657	X-RAY DIFFRACTION	99
2.7981-3.0141	0.1781	147	0.1494	2678	X-RAY DIFFRACTION	99
3.0141-3.3172	0.1706	149	0.1528	2631	X-RAY DIFFRACTION	99
3.3172-3.7969	0.1846	155	0.1454	2678	X-RAY DIFFRACTION	99
3.7969-4.7824	0.1354	121	0.1332	2693	X-RAY DIFFRACTION	99
4.7824-39.4633	0.1881	141	0.1634	2720	X-RAY DIFFRACTION	99

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	3.8326	-0.5094	1.4974	4.2117	-0.94	3.1748	0.0271	-0.1195	-0.3725	0.004	0.0822	0.1452	0.1739	-0.1199	-0.2001	0.1765	-0.0327	0.0012	0.1105	0.0245	0.2079	4.5912	-8.4044	90.2737
2	5.7582	-0.4186	2.9701	4.1977	-1.8983	7.029	0.1476	-0.2312	-0.2974	-0.043	0.4407	0.8048	0.2911	-0.5126	-0.2343	0.1672	-0.0164	-0.0092	0.1521	0.0281	0.268	-2.1488	-3.2947	87.8387
3	7.8232	-1.7781	3.7441	4.2389	-0.9787	6.9309	-0.145	-0.2912	-0.4944	0.0919	0.325	0.3624	0.0503	-0.5249	-0.208	0.1452	-0.0271	0.023	0.1371	0.0508	0.2542	-1.7488	-0.8976	91.5979
4	0.0082	0.1516	0.1622	3.3062	3.4477	3.5956	-0.0432	1.286	0.594	-0.6056	0.1726	0.4068	-0.3231	-0.0171	-0.0093	0.7673	0.2097	-0.2723	0.7965	0.1635	0.521	3.5961	-6.5404	103.7417
5	1.8608	0.2527	-0.8693	1.9062	0.8131	5.2284	0.135	-0.2016	-0.0974	0.2002	0.1243	0.2339	0.374	-0.4592	-0.1749	0.1277	-0.0229	-0.0066	0.148	0.0423	0.2108	-1.2041	1.3416	93.6737
6	2.1226	-0.3827	-0.0116	2.6498	0.8976	4.1125	0.0611	0.2981	-0.2284	-0.3386	0.0539	0.1682	0.24	-0.0396	-0.0983	0.1754	-0.0269	-0.0462	0.1573	-0	0.1941	4.2116	0.3419	78.4616
7	1.5064	-0.1248	-0.0905	2.3983	0.9118	3.8896	-0.0218	-0.2103	-0.0709	0.2936	0.0946	0.1878	0.2083	-0.2592	-0.0594	0.1272	-0.002	0.0143	0.135	0.0433	0.1551	4.5321	3.5322	96.7
8	2.907	2.7719	0.4516	6.8763	4.9824	4.9536	0.0181	0.4564	-1.1268	-0.1866	0.0013	-0.3991	1.2849	0.5757	-0.2049	0.597	-0.0131	-0.0772	0.2011	-0.0678	0.4769	7.5092	-14.7108	79.4589
9	3.6685	2.0038	1.5994	7.8715	4.902	6.3598	0.0288	0.0973	-0.2581	0.0102	0.2592	-0.2226	0.2514	0.1652	-0.3111	0.1047	0.0017	-0.0037	0.066	0.0258	0.1026	11.8255	1.1738	89.7084
10	6.4337	2.6176	-0.7875	8.869	6.0579	8.5173	-0.1596	-0.3591	0.7058	0.2128	0.4445	-0.4958	-0.2436	0.424	-0.1736	0.2092	0.0119	-0.0286	0.1671	-0.0618	0.2318	17.2445	17.4961	101.565
11	2.5556	0.7251	0.3242	4.8345	1.8332	2.3197	0.0667	0.0182	-0.5077	0.0812	0.0264	-0.0458	0.3412	-0.1937	-0.0788	0.1569	-0.0168	-0.027	0.1115	0.0426	0.1696	10.3746	-6.3391	90.2281
12	5.5597	1.242	-1.3001	7.1553	-1.5882	3.8004	-0.1468	0.1333	0.0704	-0.1292	0.1961	0.1672	-0.1606	-0.1494	-0.0588	0.1167	0.0377	-0.0168	0.116	0.0199	0.1819	0.6971	19.9252	85.6979
13	1.8835	0.4834	0.1025	2.479	1.2806	5.1771	0.0625	-0.0873	0.0987	0.1241	0.1563	0.2318	-0.2795	-0.152	-0.1518	0.1249	0.0394	0.0307	0.1133	0.0291	0.2005	1.7293	14.5333	90.6836
14	1.8266	0.1215	0.5614	2.918	1.57	3.9421	-0.0116	0.1865	0.0601	-0.2134	0.1654	0.1346	-0.2082	-0.0395	-0.1188	0.1122	-0.0073	-0.0008	0.0906	0.0451	0.1363	4.3423	11.9171	79.557
15	2.6583	-1.1081	-0.7049	3.9831	1.3086	2.8244	0.0595	0.0756	0.2806	-0.0373	0.059	-0.1588	-0.1827	-0.0528	-0.0267	0.0911	-0.0076	0.0032	0.077	0.0302	0.1184	12.4928	14.3603	84.2347
16	5.7932	-1.8945	-2.7461	7.174	2.8349	4.9556	0.1586	0.0201	0.2818	-0.105	-0.1272	-0.1744	-0.2248	0.048	-0.035	0.1074	-0.0313	0.0069	0.1404	0.0205	0.1769	21.5973	-4.294	131.9768
17	2.3955	-0.402	1.2253	2.2728	-0.5462	5.6507	0.0866	0.078	0.2252	-0.0218	0.0064	-0.1574	-0.1506	0.332	-0.0563	0.1119	-0.0245	0.0268	0.1166	-0.0131	0.1969	15.5929	-4.177	132.4745
18	2.0782	0.1959	0.4948	2.0162	-0.2782	2.7947	0.1038	0.098	0.0432	-0.112	-0.003	-0.1621	-0.0293	0.1973	-0.0964	0.0794	0.0062	0.036	0.0998	-0.0072	0.1109	14.638	-10.473	127.4582
19	8.6115	2.7668	3.6991	3.1621	0.8665	3.2921	0.0625	0.1631	-0.2197	-0.1275	0.0417	-0.1288	0.0341	0.0738	-0.065	0.1058	0.0197	0.0499	0.1068	-0.022	0.0784	11.8397	-16.6645	125.1765
20	3.9196	-1.3973	1.938	4.3168	-1.9604	4.185	0.227	-0.0255	-0.3238	-0.1053	-0.1235	0.2212	0.2567	-0.0186	-0.1111	0.1224	-0.0383	-0.0307	0.1475	0.011	0.2258	35.2001	0.9168	131.1712
21	3.8143	-1.9416	1.0172	8.9735	-4.7873	9.2776	0.3777	0.1256	-0.3536	-0.2306	-0.1056	0.2235	0.5082	-0.0368	-0.3109	0.115	-0.0296	-0.0517	0.1296	-0.0003	0.2668	40.1352	-2.0503	128.5974
22	7.0329	1.1056	-1.9746	0.1757	-0.2832	1.5123	-1.2003	0.6277	2.0612	-1.3701	0.595	1.2597	-2.9016	-0.7663	0.6888	0.7564	0.2759	-0.0738	0.8011	0.3285	0.6707	34.1466	3.162	116.313
23	1.9327	-0.217	-0.7826	2.6455	0.9827	6.7255	0.1322	-0.1522	-0.2151	0.0929	-0.0148	0.152	0.2031	-0.2888	-0.0816	0.1061	-0.0346	-0.029	0.1308	0.0355	0.2137	41.8376	1.5697	134.8356
24	3.0657	0.4115	-1.0053	2.1358	-0.3704	3.7202	0.1562	0.2126	-0.2174	-0.2054	0.0024	0.1681	0.0693	-0.3507	-0.0661	0.0964	0.0041	-0.0546	0.1061	0.0052	0.1776	42.0446	4.6	125.837
25	3.0805	1.6741	-2.3012	4.4645	-0.7544	7.1501	0.3258	-0.0886	0.2107	0.1061	-0.0323	0.28	-0.2763	-0.1791	-0.2803	0.0573	0.0195	-0.0204	0.0704	0.0013	0.1084	42.3581	11.9059	130.6963
26	7.2525	1.7982	-2.6633	3.1249	-0.709	3.059	0.1585	0.2243	0.1089	-0.1833	-0.01	0.1177	-0.0437	-0.0469	-0.1016	0.0964	0.0238	-0.0346	0.089	0.0083	0.0822	44.8291	13.3858	124.924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 16 THROUGH 27 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 28 THROUGH 37 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 38 THROUGH 44 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 45 THROUGH 49 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 50 THROUGH 60 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 61 THROUGH 78 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 79 THROUGH 97 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 98 THROUGH 102 )
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 103 THROUGH 112 )
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 113 THROUGH 122 )
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESID 123 THROUGH 134 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 15 THROUGH 49 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 50 THROUGH 78 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 79 THROUGH 97 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 98 THROUGH 135 )
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESID 15 THROUGH 37 )
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESID 38 THROUGH 78 )
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESID 79 THROUGH 112 )
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESID 113 THROUGH 134 )
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESID 16 THROUGH 37 )
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESID 38 THROUGH 44 )
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESID 45 THROUGH 49 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 50 THROUGH 78 )
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESID 79 THROUGH 102 )
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESID 103 THROUGH 112 )
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESID 113 THROUGH 135 )

-
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