PDB-5dsc: Context-independent anti-hypusine antibody FabHpu24.B in complex ...

ID or keywords:

Entry

Database: PDB / ID: 5dsc

Title

Context-independent anti-hypusine antibody FabHpu24.B in complex with hypusine

Components

Fab Hou24.B Light Chain
Fab Hpu24.B Heavy Chain
Peptide: GLY-HPU-GLY-SER-GLY

Keywords

IMMUNE SYSTEM /

hypusine /

antibody / FabHpu24.B /

eIF5A

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Oryctolagus cuniculus (rabbit)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Zhai, Q. / Carter, P.J.

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Structural Analysis and Optimization of Context-Independent Anti-Hypusine Antibodies.
Authors: Zhai, Q. / He, M. / Song, A. / Deshayes, K. / Dixit, V.M. / Carter, P.J.

History

Deposition	Sep 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 3, 2016	Group: Database references
Revision 1.2	Mar 2, 2016	Group: Database references
Revision 1.3	May 4, 2016	Group: Non-polymer description
Revision 2.0	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1	Nov 15, 2023	Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5dsc.cif.gz	646 KB	Display	PDBx/mmCIF format
PDB format	pdb5dsc.ent.gz	538.9 KB	Display	PDB format
PDBx/mmJSON format	5dsc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	5drnSC 5ds8C 5dtfC 5dubC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1riv-d 7jwp-1 6n16-3 6tcp-3 6x1u-1 6a9k-2 6bhz-1 3g6j-4 3cfj-1 6dwa-1 4jo2-1 4xcn-6 6u3z-2 5dq9-1 3v52-d 6z3k-7 5b6f-3 3i75-d 4jo1-1 1mam-d 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

5drnSC

5ds8C

5dtfC

5dubC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Fab Hpu24.B Heavy Chain

B: Fab Hou24.B Light Chain

C: Fab Hpu24.B Heavy Chain

D: Fab Hou24.B Light Chain

E: Fab Hpu24.B Heavy Chain

F: Fab Hou24.B Light Chain

H: Fab Hpu24.B Heavy Chain

L: Fab Hou24.B Light Chain

P: Peptide: GLY-HPU-GLY-SER-GLY

Q: Peptide: GLY-HPU-GLY-SER-GLY

M: Peptide: GLY-HPU-GLY-SER-GLY

N: Peptide: GLY-HPU-GLY-SER-GLY

188 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fab Hpu24.B Heavy Chain

B: Fab Hou24.B Light Chain

Q: Peptide: GLY-HPU-GLY-SER-GLY

defined by author
47 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Fab Hpu24.B Heavy Chain

D: Fab Hou24.B Light Chain

P: Peptide: GLY-HPU-GLY-SER-GLY

defined by author
47 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Fab Hpu24.B Heavy Chain

F: Fab Hou24.B Light Chain

M: Peptide: GLY-HPU-GLY-SER-GLY

defined by author
47 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

H: Fab Hpu24.B Heavy Chain

L: Fab Hou24.B Light Chain

N: Peptide: GLY-HPU-GLY-SER-GLY

defined by author
47 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.082, 167.945, 84.927
Angle α, β, γ (deg.)	90.000, 99.680, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain C
3	1	chain E
4	1	chain H
1	2	chain B
2	2	chain D
3	2	chain F
4	2	chain L
1	3	chain M
2	3	chain N
3	3	chain P
4	3	chain Q

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	PRO	PRO	chain A	A	A	2 - 210	2 - 217
2	1	GLU	GLU	ALA	ALA	chain C	C	C	2 - 209	2 - 216
3	1	PCA	PCA	SER	SER	chain E	E	E	1 - 211	1 - 218
4	1	PCA	PCA	PRO	PRO	chain H	H	G	1 - 210	1 - 217
1	2	LEU	LEU	CYS	CYS	chain B	B	B	4 - 211	4 - 215
2	2	LEU	LEU	CYS	CYS	chain D	D	D	4 - 211	4 - 215
3	2	THR	THR	CYS	CYS	chain F	F	F	5 - 211	5 - 215
4	2	LEU	LEU	ARG	ARG	chain L	L	H	4 - 208	4 - 212
1	3	GLY	GLY	GLY	GLY	chain M	M	K	3 - 7	1 - 5
2	3	GLY	GLY	GLY	GLY	chain N	N	L	3 - 7	1 - 5
3	3	GLY	GLY	GLY	GLY	chain P	P	I	3 - 7	1 - 5
4	3	GLY	GLY	GLY	GLY	chain Q	Q	J	3 - 7	1 - 5

NCS ensembles :

ID
1
2
3

#1: Antibody	Fab Hpu24.B Heavy Chain Mass: 23690.756 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Fab Hou24.B Light Chain Mass: 22838.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide	Peptide: GLY-HPU-GLY-SER-GLY Mass: 491.541 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.57 Å³/Da / Density % sol: 52.22 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 14% PEG 6000 0.5M NaCl 10mg/ml

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→49 Å / Num. obs: 73996 / % possible obs: 100 % / Redundancy: 1.9 % / R_merge(I) obs: 0.071 / Net I/σ(I): 15.4
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.415 / Mean I/σ(I) obs: 2 / % possible all: 95.2

-
Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DRN

5drn

Resolution: 2.4→49 Å / FOM work R set: 0.7712 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2481	3723	5.03 %
R_work	0.2072	70273	-
obs	0.2093	73996	99.48 %

Solvent computation

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

Displacement parameters

B_iso max: 206.54 Å² / B_iso mean: 39.9 Å² / B_iso min: 8.93 Å²

Refinement step

Cycle: final / Resolution: 2.4→49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12758	0	0	276	13034
B_iso mean	-	-	-	32.1	-
Num. residues	-	-	-	-	1710

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	13100
X-RAY DIFFRACTION	f_angle_d	0.913	17871
X-RAY DIFFRACTION	f_chiral_restr	0.034	2104
X-RAY DIFFRACTION	f_plane_restr	0.004	2266
X-RAY DIFFRACTION	f_dihedral_angle_d	11.389	4588

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3823	X-RAY DIFFRACTION	6.982	TORSIONAL
1	2	C	3823	X-RAY DIFFRACTION	6.982	TORSIONAL
1	3	E	3823	X-RAY DIFFRACTION	6.982	TORSIONAL
1	4	H	3823	X-RAY DIFFRACTION	6.982	TORSIONAL
2	1	B	3789	X-RAY DIFFRACTION	6.982	TORSIONAL
2	2	D	3789	X-RAY DIFFRACTION	6.982	TORSIONAL
2	3	F	3789	X-RAY DIFFRACTION	6.982	TORSIONAL
2	4	L	3789	X-RAY DIFFRACTION	6.982	TORSIONAL
3	1	M	28	X-RAY DIFFRACTION	6.982	TORSIONAL
3	2	N	28	X-RAY DIFFRACTION	6.982	TORSIONAL
3	3	P	28	X-RAY DIFFRACTION	6.982	TORSIONAL
3	4	Q	28	X-RAY DIFFRACTION	6.982	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4-2.4302	0.3503	129	0.3014	2441	2570	94
2.4302-2.4622	0.3282	122	0.2905	2644	2766	100
2.4622-2.4959	0.3301	135	0.2808	2610	2745	100
2.4959-2.5316	0.3724	120	0.2793	2575	2695	100
2.5316-2.5694	0.3166	124	0.2704	2701	2825	100
2.5694-2.6095	0.3117	142	0.2626	2518	2660	100
2.6095-2.6523	0.3132	126	0.2507	2663	2789	100
2.6523-2.698	0.2965	117	0.2474	2590	2707	100
2.698-2.7471	0.3029	149	0.2391	2625	2774	100
2.7471-2.7999	0.2893	140	0.2335	2578	2718	100
2.7999-2.8571	0.2482	128	0.2403	2627	2755	100
2.8571-2.9192	0.2861	135	0.2418	2572	2707	99
2.9192-2.9871	0.3016	165	0.2447	2586	2751	100
2.9871-3.0618	0.267	154	0.2389	2574	2728	99
3.0618-3.1445	0.2877	156	0.2331	2605	2761	99
3.1445-3.237	0.2861	138	0.2311	2596	2734	100
3.237-3.3415	0.2612	143	0.225	2588	2731	100
3.3415-3.4609	0.2628	131	0.2314	2637	2768	100
3.4609-3.5994	0.2636	144	0.2143	2580	2724	100
3.5994-3.7632	0.2589	123	0.2147	2624	2747	100
3.7632-3.9615	0.2088	136	0.1933	2624	2760	100
3.9615-4.2096	0.1921	119	0.1772	2647	2766	100
4.2096-4.5344	0.2105	151	0.1487	2600	2751	100
4.5344-4.9903	0.1866	138	0.1437	2620	2758	100
4.9903-5.7115	0.1858	145	0.1597	2626	2771	100
5.7115-7.1922	0.2297	165	0.1934	2601	2766	100
7.1922-48.9614	0.2017	148	0.1653	2621	2769	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	0.2163	-0.1031	-0.2185	0.7227	-0.0641	0.3025	-0.0359	-0.0869	0.0204	-0.1209	0.1504	0.2219	-0.0961	-0.0455	0.3715	0.2338	-0.0111	0.014	0.241	0.054	0.1793	18.6362	-12.9857	0.1798
2	0.0295	0.0464	-0.0704	0.267	-0.1326	0.1894	-0.0366	-0.0852	-0.1812	-0.2148	0.0663	0.0895	-0.0989	-0.0026	-0.0009	0.2745	0.0057	-0.0256	0.2589	-0.0244	0.2797	33.7023	-19.7376	3.4547
3	0.1499	-0.1372	0.0758	0.2097	-0.1284	0.0873	-0.1972	-0.035	-0.1672	0.0962	-0.0014	-0.0791	0.0377	0.0199	-0.0309	0.1971	-0.0235	0.0294	0.2525	-0.0029	0.2294	48.8919	-21.7827	5.2864
4	0.0937	-0.04	0.1068	0.0361	-0.0003	0.2181	0.114	0.015	-0.1049	-0.0491	0.0451	0.1385	0.0446	-0.0051	0.0295	0.204	-0.0009	0.0694	0.2292	0.0793	0.6602	21.8837	-41.4286	4.1709
5	0.3084	-0.2381	-0.175	0.1703	0.1364	0.1102	-0.1405	-0.18	-0.0523	0.0313	0.0686	0.2391	-0.0199	0.1397	-0.0277	0.2425	-0.012	-0.1294	0.3266	0.1265	1.0589	8.0792	-34.4766	-0.3787
6	0.0275	-0.0119	0.0774	0.0208	0.0201	0.3357	0.1837	-0.0136	-0.5016	-0.2695	0.1983	0.7649	0.0877	0.0388	0.4437	-0.0557	-0.0063	-0.2356	0.2074	0.017	0.692	17.8435	-33.2798	-4.8829
7	0.0637	-0.0732	0.0153	0.0927	-0.0145	0.0158	0.0656	0.0026	-0.0639	0.0514	-0.0307	-0.0293	0.1208	-0.0264	-0.01	0.1079	0.0661	-0.0915	0.3627	0.2892	0.5291	21.6972	-34.8021	3.5852
8	0.0528	0.0957	-0.0022	0.2733	-0.1076	0.3076	0.0132	0.0112	-0.0697	0.0821	-0.0798	0.0564	-0.1926	0.0398	-0.1529	0.1661	0.0411	-0.0643	0.1094	-0.224	0.3703	49.8195	-38.4598	9.1154
9	0.1891	-0.2169	-0.1148	0.5327	0.1382	0.0779	-0.0816	0.043	-0.1751	0.2685	0.0716	0.1629	-0.0936	0.0504	-0.0389	0.2313	-0.0043	-0.0828	0.2358	0.0028	0.2207	48.6358	-32.9088	15.9452
10	0.0025	-0.0125	-0.0083	0.0433	0.0169	0.0104	-0.1052	-0.0497	-0.1047	-0.0176	0.023	0.1848	0.0772	-0.0702	-0	0.2555	-0.0303	-0.021	0.2679	0.0314	0.2349	42.0808	-35.9045	12.6406
11	0.0087	0.0327	-0.0061	0.0241	-0.0172	0.0479	-0.0969	-0.0826	-0.1004	0.2927	0.1346	-0.2052	0.1372	0.0068	-0.0026	0.2698	0.039	-0.0669	0.3079	-0.0266	0.2627	53.5746	-35.2309	20.7894
12	0.0321	-0.0557	0.0063	0.0583	0.0244	0.0142	-0.1087	-0.0759	0.1048	-0.0809	-0.0884	-0.2179	-0.1582	0.0602	-0.0176	0.2337	-0.013	0.0481	0.2666	-0.051	0.2333	19.4312	-6.8486	44.3495
13	0.0337	0.0143	0.0253	0.3121	0.128	0.2471	0.0187	-0.204	0.0889	-0.3135	-0.04	-0.2245	-0.122	0.0428	0.0722	0.231	-0.0391	0.0854	0.231	-0.0697	-0.0963	9.125	-11.5449	38.3993
14	0.0068	-0.0487	-0.0098	0.0976	0.0434	0.022	0.2165	-0.107	0.1625	-0.1116	-0.0845	-0.0128	-0.077	-0.09	0.1238	0.1952	-0.0912	0.2447	0.231	-0.0299	-0.0677	5.8798	-7.7376	44.7252
15	0.0087	0.0655	0.065	0.0864	0.0767	0.0613	-0.1175	-0.2039	0.0661	-0.219	-0.0271	0.0153	0.1061	-0.0454	-0.1076	0.2148	0.0287	0.1167	-0.0284	-0.5077	-0.4375	12.1966	-10.8167	44.0069
16	0.0334	-0.0418	0.0022	0.0654	0.0085	0.0146	-0.0308	0.0402	0.0335	-0.1056	-0.0209	-0.0836	0.0462	-0.038	-0.0636	0.2563	-0.0354	0.024	0.2754	-0.0732	0.1267	10.2222	-16.8959	35.1624
17	0.0665	0.0404	-0.0917	0.2736	-0.3111	0.4216	-0.127	-0.0108	-0.0597	-0.0385	-0.1231	-0.1692	0.1172	0.0347	-0.1297	0.233	-0.0471	0.0044	0.2753	-0.0773	0.3783	40.859	-17.8174	52.9283
18	0.0439	0.0595	0.0315	0.0536	0.0347	0.0098	-0.0116	-0.0389	-0.1462	-0.0892	-0.029	-0.0704	0.0089	-0.0147	0	0.2411	-0.0265	0.0763	0.2677	-0.0989	0.2941	37.6309	-20.3072	47.4029
19	0.2084	-0.0681	0.2328	0.1129	0.0591	0.5744	-0.1908	-0.0256	-0.0076	-0.126	-0.1043	-0.1293	-0.1225	-0.0025	-0.0905	0.26	-0.078	0.0559	0.2793	-0.0174	0.4308	45.746	-14.2839	45.1206
20	0.0595	-0.0134	0.0895	0.0508	-0.0162	0.0539	-0.05	-0.0586	-0.3005	-0.0295	0.0592	0.3951	0.0283	-0.076	0.0029	0.1653	-0.0176	0.035	0.2144	0.0317	0.442	5.9611	-34.3214	42.1247
21	0.1856	0.0001	0.0592	0.0802	-0.0605	0.0747	0.0023	0.0201	-0.0954	-0.1551	0.0733	-0.1134	0.0306	0.1316	0.0983	0.2145	-0.0472	0.0576	0.2382	-0.0351	0.1298	15.2233	-26.6895	37.3802
22	0.0113	0.0005	-0.0155	0.0213	0.0114	0.011	0.1884	0.2463	-0.2627	-0.281	-0.0408	0.3051	0.0448	-0.2112	0.0001	0.347	-0.0276	-0.0328	0.323	-0.0746	0.52	8.0984	-32.7567	30.5589
23	0.2659	-0.1212	0.104	0.1097	0.0458	0.1265	0.0287	-0.2456	-0.3361	0.1062	0.1339	0.1318	-0.0334	0.105	0.0333	0.1922	-0.014	0.0378	0.1803	-0.0344	0.2771	9.3112	-30.5353	39.2256
24	0.2105	0.0623	0.1522	0.1941	0.1008	0.1099	0.088	-0.1032	-0.1047	0.0443	0.0176	-0.0824	0.1065	-0.1148	0.1803	0.1981	-0.009	0.0519	0.2918	0.0487	0.2276	14.3012	-31.9715	44.6412
25	0.1334	-0.0393	0.0387	0.0818	-0.0792	0.0684	0.0207	0.0768	-0.1068	0.1034	-0.0145	0.0079	0.0733	0.1825	0	0.2913	-0.0221	-0.0792	0.2626	-0.0518	0.3674	39.6854	-30.9139	56.6386
26	0.0077	-0.0078	-0.0115	0.0186	-0.0099	0.0176	-0.0571	-0.0861	-0.0196	0.1033	-0.0554	0.0657	0.3175	0.0832	-0.0001	0.3353	0.0247	-0.0864	0.2881	-0.0189	0.4995	46.8906	-36.1144	60.9462
27	0.0082	-0.0223	0.001	0.0631	-0.04	0.1863	-0.0322	0.0084	-0.1459	0.0766	0.0056	0.0215	0.1731	-0.0513	-0.0012	0.3355	0.046	-0.0362	0.2696	0.0188	0.1208	7.253	-84.6195	2.3078
28	0.1078	-0.1363	-0.042	0.6997	0.1214	0.3757	0.1202	-0.1851	0.2315	-0.0927	0.0748	-0.5992	0.1349	-0.0921	0.1729	0.2672	0.042	-0.0684	0.2767	-0.1085	0.2607	18.6198	-80.9459	-1.5223
29	0.1714	0.1144	0.0372	0.0894	0.0308	0.0212	-0.261	-0.0851	0.0339	0.1731	0.214	-0.0836	-0.1516	0.0204	-0.0367	0.4209	0.1212	-0.1826	0.2549	-0.0409	0.0683	13.7521	-84.2696	8.0277
30	0.0455	-0.042	0.0325	0.1232	0.1886	0.5384	-0.0649	-0.0988	0.0678	-0.2499	-0.0706	-0.471	-0.0067	-0.1365	-0.0698	0.2728	0.0173	0.0628	0.2048	0.0384	0.2678	16.3924	-75.13	-5.8057
31	0.7158	0.3624	0.0512	0.5139	-0.1691	0.2149	0.0101	-0.1069	0.1122	0.055	0.0763	0.2404	0.1387	-0.2207	0.008	0.3039	0.0185	0.0427	0.2408	-0.0223	0.0349	-15.1679	-73.9686	11.9012
32	0.0957	-0.0608	-0.0479	0.2307	0.1165	0.1093	0.0926	0.1305	0.07	-0.2015	-0.1958	0.3763	0.1147	-0.0998	-0.2787	0.2591	0.0392	0.0837	0.2455	-0.0563	-0.1373	-14.1698	-72.8759	5.3027
33	0.1037	0.0257	-0.1227	0.0364	-0.0222	0.0706	-0.2062	0.1849	-0.0886	0.025	0.1427	-0.4817	-0.0744	0.1166	-0.0029	0.1877	-0.0156	-0.0519	0.328	-0.0733	0.9158	20.9144	-57.0996	1.2354
34	0.2237	0.159	0.0411	0.1928	-0.0682	0.2257	0.0049	-0.0591	0.3592	-0.0551	-0.0514	-0.7185	0.0592	-0.0131	0.005	0.1816	-0.0187	0.1119	0.2005	-0.024	0.6113	16.5913	-60.1994	-6.5352
35	0.0757	0.0414	-0.1496	0.0277	-0.0428	0.2829	0.0786	0.0808	-0.1689	0.002	0.1194	-0.5366	0.0765	0.1675	0.1482	0.1486	0.0314	-0.0767	0.2917	-0.0992	0.7156	16.8818	-62.765	-1.4563
36	0.0052	0.0061	-0.0039	0.0069	-0.0077	0.0231	0.1401	-0.0386	0.0117	0.0543	0.1226	-0.0636	-0.0153	0.0628	0.2793	0.0918	-0.0381	-0.2782	0.2074	-0.3282	0.621	12.6838	-59.5989	3.5992
37	0.4529	-0.1761	0.053	0.1281	0.0204	0.0317	-0.1036	0.0685	0.1791	0.103	-0.1096	-0.1949	0.2187	-0.1067	-0.0933	0.2352	0.022	0.0004	0.2525	0.0236	0.2042	-15.4352	-56.0988	8.9732
38	0.9734	-0.5513	0.4073	0.3852	-0.2285	0.2112	-0.4012	-0.0314	0.3591	0.1528	0.1108	-0.2621	0.1412	-0.0568	-0.2084	0.3	0.0325	0.0359	0.2449	-0.0555	0.0692	-14.2753	-61.8535	15.6645
39	0.071	0.1361	0.0201	0.4596	0.0003	0.03	-0.1128	-0.0004	0.1967	-0.0423	0.1529	-0.4054	-0.0613	-0.0079	-0.1056	0.2764	0.0113	-0.0465	0.3031	-0.0335	0.1781	-7.6147	-58.8458	12.4873
40	0.6082	0.2247	-0.1551	0.2044	-0.1404	0.1258	-0.2161	-0.2143	0.3646	0.0885	0.1772	0.0356	0.1242	-0.144	-0.018	0.3135	0.03	0.0103	0.3035	-0.0051	0.1557	-19.215	-59.6791	20.6267
41	0.0385	-0.0193	0.005	0.0665	-0.0339	0.031	-0.1915	0.0769	-0.0106	0.0275	0.1373	0.0768	0.1331	-0.0228	-0.0459	0.4326	0.0384	-0.0648	0.2608	0.0167	0.1753	1.138	-81.5849	43.3858
42	0.1964	0.0672	-0.214	0.6091	-0.2279	0.3918	-0.0641	-0.0969	0.3214	-0.0749	0.2166	-0.5385	0.1484	0.0092	0.0429	0.2953	0.0631	-0.0676	0.2512	-0.0552	0.3175	12.3237	-77.8354	39.4886
43	0.1527	0.1185	-0.0224	0.1909	0.0845	0.1228	-0.2284	-0.0608	0.0419	-0.0879	0.0684	-0.1902	-0.0197	0.0246	-0.0428	0.4598	0.0959	-0.0492	0.3044	0.0173	0.1723	7.535	-81.084	49.1645
44	0.027	-0.0301	-0.0727	0.015	0.0308	0.1794	-0.0935	-0.1458	0.0064	-0.1261	0.0397	-0.2188	-0.0549	-0.0921	-0.004	0.3071	0.0024	-0.0202	0.1935	0.0464	0.2555	9.1987	-73.2042	36.0244
45	0.0079	-0.0171	0.0049	0.0319	-0.0424	0.028	-0.0386	0.0394	0.0544	-0.1797	0.0476	-0.1464	-0.0222	-0.0254	-0.0003	0.323	0.0213	0.0135	0.3001	0.0179	0.3689	10.4529	-71.3907	34.5169
46	0.0046	0.0217	0.0333	0.0253	0.037	0.0975	0.049	-0.0876	0.1228	0.1364	0.013	0.1073	-0.1745	0.0342	0.1466	0.4095	0.1186	0.153	0.3248	0.1224	0.236	-18.8414	-72.631	53.3258
47	0.0065	-0.0449	-0.0299	0.0723	0.0571	0.0405	-0.1629	0.1321	-0.0169	0.3729	0.0419	0.2079	-0.001	-0.1746	-0.1855	0.2628	0.1223	-0.0302	0.1742	0.2539	-0.5012	-17.9095	-68.8445	48.0433
48	0.0614	-0.0241	-0.0123	0.034	0.0288	0.0189	-0.1192	0.0374	0.0308	0.06	-0.0308	0.3328	-0.0746	-0.0285	-0.0016	0.1527	0.0302	-0.0335	0.2691	-0.0198	0.3467	-26.0629	-64.4335	44.9231
49	0.2579	0.2347	0.1303	0.2317	0.1504	0.1618	-0.1046	-0.0827	0.1695	-0.0256	0.0157	0.2892	0.1699	0.0288	-0.1008	0.2108	0.0208	0.0726	0.171	0.0109	0.2618	-23.5977	-75.8384	46.3204
50	0.2584	0.0544	-0.1697	0.0107	-0.0382	0.112	-0.0292	0.0375	-0.0173	0.0496	0.1702	-0.1399	0.1156	0.1388	0.2017	0.1245	0.074	-0.4048	0.2602	-0.2022	0.6502	8.1006	-49.9177	43.6031
51	0.2464	-0.0337	0.1831	0.1236	-0.2419	0.9702	-0.0867	-0.0912	0.0105	0.0598	0.2053	-0.4762	0.1095	-0.0552	0.1579	0.0631	0.0207	-0.0006	0.1501	-0.0579	0.5146	13.0466	-61.2993	37.885
52	0.0009	0.0007	-0.0037	0.0084	-0.01	0.0097	-0.0167	0.1246	0.0422	-0.1184	0.1768	-0.121	-0.0632	-0.0126	-0	0.2642	0.0049	0.1647	0.2665	0.0006	0.5614	10.5496	-56.7993	27.9166
53	0.2155	-0.0836	0.0902	0.1236	-0.0316	0.0842	0.1543	-0.0319	-0.0107	0.0555	0.0741	-0.2048	-0.044	0.009	0.2367	0.1399	-0.0131	-0.0359	0.2338	-0.0936	0.8863	15.2436	-51.8037	36.5729
54	0.2393	-0.1155	0.0842	0.1995	-0.1719	0.3627	0.0836	-0.1213	-0.0959	0.0331	0.1708	-0.3321	0.0736	0.0562	0.2948	0.1503	0.0253	-0.1309	0.1952	-0.0441	0.5795	10.2628	-59.6912	39.2385
55	0.1861	-0.0129	-0.0132	0.0173	-0.0183	0.0681	0.033	0.056	-0.0901	0.0399	0.0698	-0.1094	0.0285	0.0144	0.1352	0.24	0.0674	-0.1831	0.3486	-0.1589	0.5777	6.0787	-56.435	44.2232
56	0.3171	-0.1136	0.1766	0.0469	-0.0394	0.1078	-0.1557	0.0287	0.0851	0.3026	0.0966	-0.1633	0.2001	0.0969	-0.0581	0.4121	0.0772	0.1443	0.281	0.0257	0.2616	-21.9086	-53.0457	50.3844
57	0.2184	0.1485	0.0544	0.1796	-0.1476	0.2715	-0.3236	-0.0789	-0.1262	0.1285	-0.1183	0.1236	0.1442	0.0232	-0.5317	0.671	0.1838	0.4528	0.2837	0.1383	0.0904	-24.1472	-65.7824	59.4002
58	0.01	-0.0123	-0.0013	0.0256	-0.0019	0.005	-0.1711	-0.0524	0.0108	0.2886	0.1943	-0.0941	-0.0024	-0.0126	0.0001	0.4386	0.0856	-0.0317	0.3132	-0.0183	0.3331	-15.8399	-50.5195	55.2446
59	0.1885	0.0075	0.1581	0.0151	0.0076	0.1274	0.0408	0.1701	-0.0091	0.1554	0.0317	-0.0191	-0.0267	0.0599	0.0479	0.6876	0.3782	-0.1677	0.4593	0.0318	-0.0099	-16.1976	-56.8578	64.0071
60	0.3388	0.0642	0.1691	0.1534	0.0944	0.1994	-0.5583	-0.038	0.2393	0.7677	0.0977	0.0735	-0.0398	0.1038	-0.7213	0.6705	0.1772	0.2705	0.1933	-0.1447	0.0169	-19.1506	-56.7918	57.3203
61	0.2067	-0.1481	0.1008	0.1297	0.002	0.4152	-0.3699	-0.1264	-0.0327	0.3212	-0.1174	0.0811	0.1036	-0.0976	-0.1679	0.6995	0.1474	0.2666	0.3893	-0.193	0.5593	-25.89	-50.1309	59.2482
62	0.0256	-0.015	0.0129	0.0074	-0.0076	0.004	0.0066	0.0122	-0.0276	0.0089	-0.0237	-0.0162	-0.0666	-0.1117	0.0001	0.193	0.0207	-0.0322	0.3102	-0.1077	0.2613	-5.94	-14.9573	35.7686
63	0.0011	-0.0005	-0.0052	0	0.0053	0.0544	0.0294	0.0456	-0.0119	0.0135	0.019	0.0033	0.0474	-0.0646	0.0063	0.2396	-0.0348	-0.344	0.3026	0.0363	0.8615	1.5487	-17.9033	-5.3176
64	0.0071	-0.0007	-0.0038	0.0024	0.0006	0.0013	0.0085	0.0132	0.0072	-0.0511	-0.0065	-0.0195	0.0071	0.062	0.0001	0.4114	0.0826	0.1165	0.4564	-0.0328	1.1999	33.1843	-76.369	-5.3464
65	0.0292	-0.01	-0.008	0.0053	0.0052	0.0035	0.0086	0.0589	0.0114	-0.052	0.0062	-0.021	0.0437	0.0902	0.0002	0.3473	0.0646	0.0928	0.4467	-0.0493	0.9078	26.6232	-73.2168	35.506

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 98 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 99 through 134 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 135 through 210 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 17 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 18 through 32 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 33 through 95B)	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 96 through 107 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 108 through 121 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 122 through 149 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 150 through 173 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 174 through 211 )	B
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 17 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 18 through 59 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 60 through 74 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 75 through 98 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 99 through 109 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 110 through 145 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 146 through 185 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 186 through 209 )	C
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 4 through 32 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 33 through 48 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 49 through 69 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 70 through 95B)	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 96 through 107 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 108 through 187 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 188 through 211 )	D
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 2 through 17 )	E
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 18 through 74 )	E
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 75 through 87 )	E
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 88 through 109 )	E
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 110 through 134 )	E
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 135 through 211 )	E
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 5 through 32 )	F
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 33 through 75 )	F
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 76 through 95B)	F
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 96 through 107 )	F
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 108 through 121 )	F
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 122 through 149 )	F
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 150 through 173 )	F
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 174 through 211 )	F
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 2 through 17 )	H
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 18 through 74 )	H
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 75 through 87 )	H
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 88 through 98 )	H
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 99 through 109 )	H
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 110 through 135 )	H
47	X-RAY DIFFRACTION	47	chain 'H' and (resid 136 through 175 )	H
48	X-RAY DIFFRACTION	48	chain 'H' and (resid 176 through 190 )	H
49	X-RAY DIFFRACTION	49	chain 'H' and (resid 191 through 210 )	H
50	X-RAY DIFFRACTION	50	chain 'L' and (resid 4 through 24 )	L
51	X-RAY DIFFRACTION	51	chain 'L' and (resid 25 through 48 )	L
52	X-RAY DIFFRACTION	52	chain 'L' and (resid 49 through 61 )	L
53	X-RAY DIFFRACTION	53	chain 'L' and (resid 62 through 75 )	L
54	X-RAY DIFFRACTION	54	chain 'L' and (resid 76 through 95B)	L
55	X-RAY DIFFRACTION	55	chain 'L' and (resid 96 through 107 )	L
56	X-RAY DIFFRACTION	56	chain 'L' and (resid 108 through 121 )	L
57	X-RAY DIFFRACTION	57	chain 'L' and (resid 122 through 137 )	L
58	X-RAY DIFFRACTION	58	chain 'L' and (resid 138 through 149 )	L
59	X-RAY DIFFRACTION	59	chain 'L' and (resid 150 through 162 )	L
60	X-RAY DIFFRACTION	60	chain 'L' and (resid 163 through 197 )	L
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 198 through 208 )	L
62	X-RAY DIFFRACTION	62	chain 'P' and (resid 3 through 7 )	P
63	X-RAY DIFFRACTION	63	chain 'Q' and (resid 3 through 7 )	Q
64	X-RAY DIFFRACTION	64	chain 'M' and (resid 3 through 7 )	M
65	X-RAY DIFFRACTION	65	chain 'N' and (resid 3 through 7 )	N

-
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