PDB-5cer: Bd0816 Predatory Endopeptidase from Bdellovibrio bacteriovorus in...

ID or keywords:

Entry

Database: PDB / ID: 5cer

Title

Bd0816 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460

Components

Bd0816
Bd3460

Keywords

IMMUNE SYSTEM / transpeptidase and ankyrin repeat

Function / homology

Function and homology information

peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / proteolysis
Similarity search - Function

Biological species

Bdellovibrio bacteriovorus HD100 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Lovering, A.L. / Cadby, I.T. / Lambert, C. / Sockett, R.E.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2015
Title: Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus.
Authors: Lambert, C. / Cadby, I.T. / Till, R. / Bui, N.K. / Lerner, T.R. / Hughes, W.S. / Lee, D.J. / Alderwick, L.J. / Vollmer, W. / Sockett, E.R. / Lovering, A.L.

History

Deposition	Jul 7, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 9, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 16, 2015	Group: Database references
Revision 1.2	Aug 30, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cer.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb5cer.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5cer.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/ce/5cer ftp://data.pdbj.org/pub/pdb/validation_reports/ce/5cer	HTTPS FTP

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Related structure data

Related structure data	5ceaC 5cebC 5cecSC 5cedC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cec-d 4hdo-d 5hyh-1 4fk3-d 4hdq-d 3r8i-d 5w7c-2 6oq4-d 1tnb-5 6p4x-4 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) 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

5ceaC

5cebC

5cecSC

5cedC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: Bd0816

B: Bd3460

C: Bd0816

D: Bd3460

E: Bd0816

F: Bd3460

G: Bd0816

H: Bd3460

I: Bd0816

J: Bd3460

K: Bd0816

L: Bd3460

hetero molecules

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

1

A: Bd0816

B: Bd3460

defined by author&software
65.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Bd0816

D: Bd3460

defined by author&software
65.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Bd0816

F: Bd3460

defined by author&software
65.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Bd0816

H: Bd3460

defined by author&software
65.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Bd0816

J: Bd3460

hetero molecules

defined by author&software
65.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Bd0816

L: Bd3460

defined by author&software
65.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	237.450, 212.320, 90.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	1 - 401
2	1	C	1 - 401
1	2	A	1 - 401
2	2	E	1 - 401
1	3	A	1 - 398
2	3	G	1 - 398
1	4	A	1 - 401
2	4	I	1 - 401
1	5	A	1 - 399
2	5	K	1 - 399
1	6	B	28 - 220
2	6	D	28 - 220
1	7	B	28 - 220
2	7	F	28 - 220
1	8	B	28 - 220
2	8	H	28 - 220
1	9	B	28 - 220
2	9	J	28 - 220
1	10	B	28 - 220
2	10	L	28 - 220
1	11	C	1 - 401
2	11	E	1 - 401
1	12	C	1 - 398
2	12	G	1 - 398
1	13	C	1 - 401
2	13	I	1 - 401
1	14	C	1 - 399
2	14	K	1 - 399
1	15	D	28 - 220
2	15	F	28 - 220
1	16	D	28 - 220
2	16	H	28 - 220
1	17	D	28 - 220
2	17	J	28 - 220
1	18	D	28 - 220
2	18	L	28 - 220
1	19	E	1 - 398
2	19	G	1 - 398
1	20	E	1 - 401
2	20	I	1 - 401
1	21	E	1 - 399
2	21	K	1 - 399
1	22	F	28 - 220
2	22	H	28 - 220
1	23	F	28 - 220
2	23	J	28 - 220
1	24	F	28 - 220
2	24	L	28 - 220
1	25	G	1 - 398
2	25	I	1 - 398
1	26	G	1 - 398
2	26	K	1 - 398
1	27	H	28 - 220
2	27	J	28 - 220
1	28	H	28 - 220
2	28	L	28 - 220
1	29	I	1 - 399
2	29	K	1 - 399
1	30	J	28 - 220
2	30	L	28 - 220

NCS ensembles :

#1: Protein	Bd0816 Mass: 44521.594 Da / Num. of mol.: 6 / Fragment: Bd0816 / Mutation: K26M, S58A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria) Gene: Bd0816 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6MPN2, serine-type D-Ala-D-Ala carboxypeptidase
#2: Protein	Bd3460 Mass: 20550.508 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria) Gene: Bd3460 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MHS9
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1356 / 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: 2.63 Å³/Da / Density % sol: 53.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Na HEPES pH 7.5, 0.2M MgCl2, 25% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92001 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92001 Å / Relative weight: 1
Reflection	Resolution: 2.48→100 Å / Num. obs: 153169 / % possible obs: 99 % / Redundancy: 13.5 % / R_sym value: 0.156 / Net I/σ(I): 15.1
Reflection shell	Redundancy: 14 % / Mean I/σ(I) obs: 15.1 / R_sym value: 0.753

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5CEC

5cec

Resolution: 2.48→100 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.888 / SU B: 18.896 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.472 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2491	7978	5 %	RANDOM
R_work	0.215	-	-	-
obs	0.2167	153169	98.79 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso max: 238.35 Å² / B_iso mean: 43.935 Å² / B_iso min: 6.17 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.18 Å²	-0 Å²	0 Å²
2-	-	-0.49 Å²	-0 Å²
3-	-	-	-1.69 Å²

Refinement step

Cycle: final / Resolution: 2.48→100 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27359	0	4	1356	28719
B_iso mean	-	-	36.78	34.22	-
Num. residues	-	-	-	-	3561

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	27725
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	27363
X-RAY DIFFRACTION	r_angle_refined_deg	1.683	1.966	37344
X-RAY DIFFRACTION	r_angle_other_deg	1.861	3	63069
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.437	5	3548
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.435	26.017	1175
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.141	15	5239
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.982	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	4324
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	31455
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	5917
X-RAY DIFFRACTION	r_mcbond_it	1.117	2.017	14231
X-RAY DIFFRACTION	r_mcbond_other	1.117	2.017	14230
X-RAY DIFFRACTION	r_mcangle_it	1.819	3.022	17763

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	49732	0.08
1	2	C	49732	0.08
2	1	A	49000	0.08
2	2	E	49000	0.08
3	1	A	49228	0.09
3	2	G	49228	0.09
4	1	A	49128	0.08
4	2	I	49128	0.08
5	1	A	48424	0.1
5	2	K	48424	0.1
6	1	B	24028	0.08
6	2	D	24028	0.08
7	1	B	23806	0.08
7	2	F	23806	0.08
8	1	B	23846	0.09
8	2	H	23846	0.09
9	1	B	23690	0.1
9	2	J	23690	0.1
10	1	B	23660	0.09
10	2	L	23660	0.09
11	1	C	49172	0.09
11	2	E	49172	0.09
12	1	C	49116	0.09
12	2	G	49116	0.09
13	1	C	49124	0.09
13	2	I	49124	0.09
14	1	C	48946	0.09
14	2	K	48946	0.09
15	1	D	23848	0.09
15	2	F	23848	0.09
16	1	D	23882	0.09
16	2	H	23882	0.09
17	1	D	23854	0.09
17	2	J	23854	0.09
18	1	D	23606	0.1
18	2	L	23606	0.1
19	1	E	49492	0.08
19	2	G	49492	0.08
20	1	E	49564	0.08
20	2	I	49564	0.08
21	1	E	49158	0.08
21	2	K	49158	0.08
22	1	F	23978	0.08
22	2	H	23978	0.08
23	1	F	23626	0.09
23	2	J	23626	0.09
24	1	F	24038	0.08
24	2	L	24038	0.08
25	1	G	49358	0.09
25	2	I	49358	0.09
26	1	G	49330	0.08
26	2	K	49330	0.08
27	1	H	23810	0.09
27	2	J	23810	0.09
28	1	H	23914	0.09
28	2	L	23914	0.09
29	1	I	49386	0.08
29	2	K	49386	0.08
30	1	J	23560	0.1
30	2	L	23560	0.1

LS refinement shell

Resolution: 2.48→2.544 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	563	-
R_work	0.257	11331	-
all	-	11894	-
obs	-	-	99.44 %

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	0.5675	0.2069	0.3872	0.8719	0.3077	0.941	-0.0444	-0.0294	0.0326	-0.0099	0.0105	-0.1045	-0.0902	0.2011	0.0339	0.0347	-0.0371	-0.0259	0.1508	0.0003	0.0425	-39.949	30.864	-28.22
2	2.8693	1.6108	-0.3375	1.4655	-2.4881	9.6011	0.0554	0.2035	-0.0045	-0.059	-0.0351	0.0062	0.2149	0.4945	-0.0203	0.28	-0.0174	0.0087	0.2791	-0.0088	0.1654	-31.343	42.618	-37.565
3	2.4374	0.7105	-0.5453	2.7126	-0.873	3.9475	-0.0945	0.0732	0.2573	0.0421	0.0762	-0.1648	-0.1888	0.0233	0.0183	0.1357	-0.0577	-0.0891	0.1803	-0.0545	0.1456	-34.427	42.542	-16.529
4	1.1837	0.0575	0.3318	1.3177	0.2542	1.5039	0.0237	0.0177	0.021	-0.0196	0.0431	-0.006	0.1024	0.1111	-0.0667	0.0537	-0.0146	-0.0322	0.09	-0.0113	0.0259	-47.383	23.64	-35.201
5	1.0358	-0.5325	0.1019	7.2574	-1.7419	2.6678	0.0196	-0.1073	0.0093	0.0392	0.0824	0.3178	-0.0231	0.0251	-0.102	0.0254	-0.0093	-0.0233	0.0921	-0.0054	0.0447	-64.087	19.77	-38.086
6	12.7706	6.8803	4.8619	4.3542	2.1316	3.3954	0.4296	-0.6212	0.0115	0.2563	-0.3961	-0.0766	0.2298	-0.2725	-0.0335	0.1552	-0.0316	-0.0111	0.1427	-0.008	0.024	-43.857	25.915	-15.418
7	6.6121	2.3865	2.5123	9.4275	-4.0526	9.6526	-0.4918	0.2467	1.063	-0.1855	0.095	-0.646	-1.1078	0.0446	0.3968	0.3177	-0.0538	-0.0755	0.2247	0.02	0.4602	-55.656	53.202	-37.895
8	1.6407	-0.4399	0.2394	4.2505	-1.2778	2.589	-0.0435	-0.1563	0.4286	0.0736	-0.1914	-0.2404	-0.3512	0.0061	0.2349	0.1633	0.0116	-0.112	0.115	-0.0299	0.1811	-66.728	45.879	-34.972
9	0.1634	0.1386	0.2544	5.3344	3.9385	7.215	0.0135	-0.1273	0.0607	0.4117	0.1536	-0.1052	0.0932	-0.2084	-0.1671	0.0819	0.0427	-0.0456	0.1931	-0.0229	0.1305	-75.97	39.403	-33.592
10	2.0929	0.7418	0.3461	4.1099	0.1691	0.4405	-0.0369	-0.2588	0.0177	0.441	-0.0323	0.2011	0.0183	-0.1551	0.0692	0.0706	0.0066	-0.0135	0.2699	-0.0189	0.1207	-79.263	29.526	-30.562
11	4.2207	-1.5283	1.3528	2.575	1.5937	5.9292	0.0579	-0.4135	-0.6381	0.0981	0.0071	0.3035	-0.2013	-0.404	-0.065	0.1	-0.0446	0.0081	0.2168	0.0607	0.1811	-84.1	19.293	-31.353
12	15.6122	-1.2691	0.0464	1.1739	-2.017	3.8508	0.131	-1.4124	-1.4738	0.3335	-0.0789	0.2357	-0.5684	0.264	-0.0521	0.5275	-0.1126	0.2283	0.5387	0.0218	0.7081	-82.239	11.641	-25.741
13	0.4223	0.0449	0.3999	0.9865	0.1399	1.4648	0.1086	0.2552	-0.0408	-0.1206	0.0471	-0.3504	0.3413	0.4569	-0.1557	0.2046	0.083	-0.0283	0.2582	-0.0387	0.1724	-41.635	-15.779	-70.626
14	5.3156	2.3665	-0.0564	4.7468	0.6076	4.4622	0.0953	0.4935	0.1052	0.1314	-0.0105	-1.0122	0.2256	0.8854	-0.0848	0.2735	0.2174	-0.0827	0.6476	-0.1024	0.5448	-26.836	-20.929	-66.254
15	8.4009	1.4265	1.0356	1.5145	-0.5566	3.6457	0.1626	-0.2767	-0.2431	0.229	-0.0521	-0.1915	0.5623	0.2988	-0.1105	0.5634	0.1591	-0.1742	0.1409	-0.0712	0.1717	-40.6	-35.796	-67.128
16	5.8172	1.2559	2.1324	3.9805	1.7998	1.2754	-0.0577	0.1497	-0.3314	-1.027	0.4348	-0.6966	-0.333	0.2984	-0.3771	0.5446	0.2749	0.0827	1.0364	-0.0873	0.4389	-24.644	-25.012	-83.849
17	1.0742	-0.2844	0.2318	1.0135	0.2227	1.8204	0.0312	0.0671	0.0054	-0.0711	0.0049	-0.0622	0.0659	0.1452	-0.0361	0.0752	0.0016	-0.048	0.0479	-0.0122	0.049	-52.374	-6.013	-63.916
18	6.0563	-4.8149	-3.71	4.9404	3.5245	3.7792	0.0255	0.1137	-0.4476	-0.1121	-0.0268	0.2886	0.1534	0.041	0.0012	0.1989	-0.057	-0.0854	0.0755	0.0027	0.1009	-58.596	-19.333	-67.782
19	11.0551	4.245	5.2369	6.1867	7.6511	9.7984	0.1779	0.114	0.0585	0.528	0.3644	-0.716	0.6616	0.8022	-0.5423	0.2811	0.1132	-0.1235	0.5309	0.1945	0.5641	-31.089	-15.303	-44.159
20	2.2517	0.5333	1.6493	7.2424	-1.8907	1.9768	-0.042	-0.1336	-0.073	-0.1499	0.0394	-0.3246	0.0736	-0.0144	0.0026	0.1651	0.1129	-0.0796	0.3614	-0.0462	0.1473	-38.47	-10.915	-36.864
21	4.1518	-1.2434	0.2612	10.6673	-0.762	3.128	0.0395	-0.0039	-0.4384	0.5727	0.0226	-0.1128	0.6574	0.4032	-0.0621	0.3401	0.1036	-0.0583	0.1289	-0.0416	0.0912	-40.809	-21.24	-42.694
22	2.2304	-0.0449	-0.0684	2.9956	-0.6313	1.546	0.0742	-0.1891	-0.3082	0.1441	-0.0528	-0.0582	0.4921	0.0822	-0.0214	0.2886	0.0587	-0.0751	0.0639	0.0069	0.071	-50.589	-15.814	-37.901
23	2.8024	-0.0521	0.0499	2.3208	-0.8095	2.922	0.1009	-0.0089	-0.1731	0.0482	0.0365	-0.0649	0.5153	-0.1371	-0.1374	0.1762	-0.0727	-0.0741	0.0874	0.0175	0.0551	-66.385	-16.247	-39.658
24	2.9707	-0.8153	1.3549	4.3743	0.1472	6.0251	0.0073	-0.2201	-0.1813	0.0343	-0.0115	0.6104	0.3407	-0.6551	0.0042	0.0853	-0.068	0.0028	0.2689	0.0397	0.1546	-78.481	-9.201	-41.42
25	0.3008	0.3456	-0.1496	0.8128	0.2839	0.6129	-0.0345	0.0442	0.1072	-0.1605	0.1688	0.0971	-0.0936	0.0521	-0.1343	0.117	-0.0706	-0.0637	0.1466	0.072	0.113	-69.381	35.099	-71.379
26	0.7405	0.2815	-0.3728	3.2693	-0.4511	2.2708	-0.0494	0.0847	0.0506	-0.9042	0.2078	0.285	0.1731	-0.0731	-0.1584	0.5033	-0.1604	-0.1816	0.1359	0.0824	0.1044	-74.065	42.745	-95.617
27	1.6858	0.0546	-0.7695	3.5628	-0.744	3.0276	-0.0816	0.119	0.0584	-0.6493	0.2202	0.3437	0.1202	-0.2336	-0.1386	0.3979	-0.1082	-0.2351	0.2387	0.0671	0.1699	-78.224	50.578	-93.746
28	0.7427	0.1673	0.1071	2.0365	-0.2239	1.4875	-0.0513	-0.0388	0.0456	-0.1516	0.0767	0.1341	-0.058	-0.0015	-0.0254	0.1129	-0.0632	-0.0746	0.1318	0.0584	0.0556	-70.706	29.895	-70.683
29	2.1877	-2.4267	-4.3533	4.7555	5.6815	9.587	-0.2268	-0.0575	0.0126	0.2617	0.1815	0.3028	0.5733	0.0395	0.0452	0.1021	-0.0889	-0.0504	0.2247	0.054	0.0887	-79.666	17.293	-64.33
30	1.7307	2.0894	-2.1479	7.8239	-6.3786	6.8107	-0.0512	0.1148	0.2068	0.0482	0.468	0.2984	-0.1287	-0.3966	-0.4168	0.1097	-0.0687	-0.1357	0.1612	0.1248	0.3469	-85.385	44.66	-79.685
31	7.4271	-2.319	-2.7087	6.7448	-0.1952	5.2574	-0.0512	0.7776	-0.4018	-1.162	-0.282	-0.3679	0.0329	0.0759	0.3332	0.4648	-0.1473	-0.0084	0.4053	0.0451	0.1932	-70.711	16.125	-98.239
32	3.2224	-2.0947	1.3711	4.4785	-0.2168	6.1425	0.1312	0.3298	0.12	-0.8051	-0.042	0.0891	0.1257	-0.0278	-0.0892	0.3979	-0.1205	-0.1276	0.2211	0.0004	0.0851	-77.231	11.653	-93.55
33	2.1619	1.0598	0.2055	2.8242	0.7925	1.5877	-0.1678	0.1694	0.0108	-0.42	0.1171	0.5375	0.0388	-0.1011	0.0507	0.2252	-0.1064	-0.1709	0.1595	0.0426	0.1783	-83.963	7.884	-81.812
34	2.8084	-2.8442	4.5907	4.2729	-6.1448	9.154	0.2834	-0.2306	-0.2578	0.2165	0.7694	1.0742	-0.1911	-0.8641	-1.0528	0.3423	0.0567	-0.1379	0.6212	0.2755	1.4491	-96.07	9.383	-79.494
35	0.6783	0.9611	0.2599	5.4526	2.017	3.0591	0.0618	-0.1058	0.0061	0.3537	-0.1011	0.6978	0.2419	-0.5186	0.0393	0.0873	-0.1054	0.005	0.2577	0.0481	0.2411	-91.715	4.899	-63.57
36	5.9233	6.7812	-10.637	7.8916	-12.3452	19.3747	0.1307	0.0311	0.4065	0.0226	0.383	0.4522	0.0343	-0.4805	-0.5137	0.4665	-0.1951	0.1764	0.8864	-0.0655	0.821	-98.132	11.607	-55.585
37	1.3443	0.0815	-0.2912	0.5066	0.1663	0.836	0.0955	0.094	0.3662	-0.1731	0.0163	-0.0794	-0.3191	0.2656	-0.1118	0.2046	-0.0951	0.0589	0.2361	-0.0104	0.2126	-101.704	63.422	-68.017
38	5.0889	3.4719	-1.8402	2.4244	-1.0293	3.0995	-0.047	0.4883	1.1827	0.0303	0.2886	0.7717	-0.2575	-0.2958	-0.2416	0.4825	-0.129	0.0888	0.4052	0.0434	0.5986	-102.674	77.97	-63.564
39	3.7611	0.3076	-0.4997	3.068	-0.1291	2.0872	-0.0728	-0.1161	0.4223	0.1227	0.1385	-0.114	-0.5555	0.3465	-0.0657	0.2756	-0.1785	0.0948	0.4148	-0.1181	0.3173	-86.556	71.478	-66.62
40	1.5465	0.2657	-0.6589	1.1885	-0.2624	2.4267	0.0723	0.1981	0.1611	-0.0965	0.0309	-0.0884	-0.307	0.1125	-0.1032	0.1013	-0.0645	0.0479	0.156	-0.0417	0.139	-108.44	56.322	-64.928
41	1.1814	-0.9512	-0.9687	3.9726	2.5164	3.0054	-0.0651	0.0287	0.0546	0.2729	0.1239	-0.1121	0.1394	0.0696	-0.0587	0.0368	-0.0407	0.0124	0.1559	-0.0298	0.1297	-112.34	44.532	-49.936
42	4.6133	6.6262	-4.3671	10.1716	-6.3105	4.1636	-0.093	-0.0266	0.0276	-0.147	0.161	-0.0974	0.0653	0.0833	-0.068	0.0587	-0.0432	0.0346	0.3358	-0.0738	0.218	-93.925	48.971	-65.41
43	1.3282	-1.7139	-3.1009	8.3204	0.5301	10.6147	0.3461	-0.0833	0.3284	0.3831	0.0062	-0.0467	-1.1968	-0.0124	-0.3523	0.3827	-0.0716	0.085	0.2565	-0.077	0.4295	-103.98	75.404	-41.227
44	14.1896	5.606	0.4093	3.1634	1.8926	3.1781	0.0277	-0.1399	0.2973	-0.3026	-0.164	0.1706	-0.5335	-0.2488	0.1362	0.2701	-0.0395	0.0715	0.3247	-0.1124	0.2282	-107.547	68.016	-33.573
45	11.321	2.558	2.9251	7.0187	0.2067	2.3565	-0.286	0.1519	0.2042	-0.1312	0.2676	-0.2601	-0.4163	0.313	0.0184	0.1495	-0.1685	0.0739	0.355	-0.0656	0.1873	-96.954	66.498	-39.279
46	0.7916	-0.4883	-0.499	2.5618	0.2826	1.216	-0.0127	-0.2295	0.0368	0.1725	0.0081	-0.1841	0.0266	0.3284	0.0046	0.0214	-0.0354	-0.0173	0.3142	-0.0704	0.1395	-99.959	46.861	-34.919
47	1.1626	-0.4584	0.2584	2.4863	0.5986	14.478	0.0311	-0.0664	-0.3348	0.1283	0.0207	0.2177	0.7005	0.129	-0.0518	0.09	-0.0223	0.0151	0.1914	0.014	0.3019	-107.65	28.717	-35.99
48	12.9702	-0.8533	-13.3825	24.3315	-4.3108	14.9619	-0.7775	-0.2126	-0.6987	-0.0457	0.1153	-0.3449	0.8977	0.1433	0.6623	0.5318	0.0584	-0.2112	0.3102	0.1006	0.4803	-98.537	23.227	-40.356
49	0.6347	-0.1552	-0.1354	1.2022	0.4136	1.3959	0.0258	-0.0846	0.0407	-0.1852	0.0118	-0.0022	-0.242	-0.1195	-0.0376	0.0715	-0.0047	0.0062	0.1353	-0.0208	0.0263	-140.004	59.242	-29.206
50	0.6583	0.2533	-0.8064	1.9993	1.2485	2.9233	-0.0387	-0.0013	-0.0369	-0.1646	-0.1753	0.4178	-0.3362	-0.5354	0.214	0.1387	0.1219	0.0396	0.4526	-0.0261	0.2127	-158.608	65.899	-17.306
51	3.7862	-0.3466	0.8447	2.9228	-0.9342	4.863	-0.0162	0.0293	0.0552	-0.0142	-0.0154	0.4122	-0.0763	-0.3342	0.0316	0.0959	0.0222	0.0481	0.2999	-0.106	0.1345	-156.243	68.04	-8.793
52	1.6868	-0.7304	-0.637	2.2689	0.6066	1.9025	0.072	-0.0545	-0.028	-0.1445	-0.0351	-0.014	-0.0005	-0.0385	-0.0369	0.031	-0.014	0.0046	0.111	-0.0313	0.02	-139.931	56.298	-29.797
53	4.8296	0.8676	1.1686	0.9676	0.4166	1.5293	0.1099	-0.0469	-0.382	-0.0585	-0.0154	-0.1326	0.0607	-0.013	-0.0945	0.0956	-0.0052	0.0212	0.0807	-0.0249	0.0525	-136.348	39.987	-34.168
54	6.5254	-8.7353	-1.7712	12.8438	3.8996	4.5148	-0.1213	-0.1311	0.0393	0.4829	0.1001	-0.2278	0.3867	-0.0797	0.0212	0.1522	0.0219	-0.0073	0.2791	-0.0154	0.119	-141.968	59.563	-10.058
55	5.8543	-0.5738	0.8395	11.5101	5.4728	9.2481	0.4784	0.0947	0.2525	-0.0113	-0.5991	0.7729	-0.0325	-1.0725	0.1207	0.2134	0.0149	0.075	0.3899	-0.1213	0.3383	-166.818	44.57	-32.146
56	3.7315	-0.9364	-3.6419	0.3687	0.104	8.4892	0.1192	0.0719	0.3112	0.0575	0.0398	-0.105	-0.69	-0.3222	-0.159	0.1903	0.0006	0.0493	0.4459	-0.0676	0.4008	-172.476	38.117	-35.01
57	4.5633	2.5779	4.1148	4.2242	6.1313	9.0756	-0.6889	0.0099	0.7774	-0.1275	-0.5708	0.9926	-0.3772	-0.5794	1.2597	0.3865	-0.1492	0.0997	0.4571	-0.2658	0.5214	-159.741	36.777	-32.966
58	3.1327	-0.6512	0.9617	2.662	0.1764	2.4149	-0.0103	-0.3833	0.0747	0.6481	-0.1105	0.0953	0.1513	-0.3646	0.1207	0.3207	-0.1553	0.0859	0.2105	-0.047	0.0342	-154.806	29.609	-27.643
59	4.3331	0.4452	0.8375	4.1403	0.4687	1.4077	0.1615	-0.3421	-0.5104	0.5492	-0.0467	-0.6031	0.489	0.0861	-0.1148	0.5969	-0.0307	-0.0984	0.1803	0.0607	0.1981	-136.839	19.436	-27.26
60	2.8374	-4.5473	-1.6834	7.2879	2.6971	1.0158	-0.2872	-0.1533	-0.1763	0.4163	0.212	0.2851	0.1067	0.1794	0.0752	0.5661	-0.0796	-0.1939	0.5248	0.0406	0.6601	-124.616	20.996	-21.847
61	0.9242	0.6085	-1.186	0.9468	-0.069	2.4895	0.0159	0.1745	0.0869	-0.0158	-0.0038	0.1203	-0.0816	-0.3677	-0.0121	0.0421	0.0093	0.0197	0.0962	0.0157	0.062	-148.103	33.071	-64.274
62	2.1752	0.7382	0.791	1.6856	0.5078	4.3075	-0.0305	0.2086	-0.0151	-0.3471	0.1236	0.2849	0.5492	-1.3171	-0.0931	0.3314	-0.2105	-0.0552	0.6064	0.0856	0.0996	-160.637	25.947	-91.038
63	2.5171	0.5584	-0.9839	10.4235	1.1691	7.9387	0.1077	0.4791	0.1838	-1.0057	-0.0774	-0.7157	-0.1321	-0.6773	-0.0303	0.3101	-0.0492	0.0219	0.4592	0.0963	0.2071	-153.809	29.442	-93.549
64	1.1833	-0.8321	0.5306	8.1913	-2.5033	6.2925	-0.0347	0.3696	0.0903	-0.1551	-0.0497	0.1009	1.0487	-0.4871	0.0845	0.2856	-0.2807	-0.022	0.4953	-0.0159	0.1962	-160.786	20.012	-91.54
65	1.4709	-0.1039	-0.0227	1.4623	-0.3325	2.9016	-0.0127	0.1965	0.1869	-0.0547	0.0578	0.275	-0.0121	-0.6663	-0.0451	0.0621	-0.0069	0.0198	0.2567	0.0313	0.099	-154.459	35.249	-75.047
66	1.2114	-0.0812	-0.3698	0.6297	-0.5747	2.6921	0.0268	-0.0075	-0.0801	0.0386	-0.001	-0.0102	0.3568	-0.1679	-0.0257	0.1108	-0.0526	0.015	0.0549	-0.0292	0.0515	-142.016	24.739	-64.271
67	11.7906	2.3422	0.1471	4.6747	-3.628	8.0697	0.048	0.7796	0.6223	-0.144	0.4349	0.194	-0.4751	-0.4814	-0.4829	0.3567	0.0658	0.0746	0.2455	0.0522	0.1999	-131.445	33.026	-90.592
68	23.0014	0.7293	-5.4584	6.0708	0.646	1.7072	-0.4294	1.05	1.2389	-1.2115	0.3003	0.1026	0.0806	-0.547	0.1291	0.7202	-0.0348	0.1121	0.6222	-0.197	0.6705	-129.855	31.452	-99.869
69	6.3411	2.6891	-0.2867	5.2674	0.1092	5.2086	-0.1156	0.6775	-0.072	-0.6937	0.1788	-0.0493	0.1096	-0.0693	-0.0632	0.2283	-0.0223	0.0475	0.2227	-0.0059	0.0503	-125.801	25.944	-89.03
70	1.988	0.2514	-0.8111	2.5813	-0.6147	4.0867	-0.0056	0.2168	-0.3107	-0.1574	0.1133	-0.2049	0.2945	0.0715	-0.1077	0.0893	0.0101	0.0345	0.0865	-0.0704	0.1167	-121.755	19.582	-76.947
71	2.7285	-0.3511	-0.1585	2.849	0.6031	3.7363	-0.1099	-0.2608	-0.4218	0.0424	-0.0007	-0.2599	0.5741	0.4496	0.1106	0.134	0.0876	0.015	0.119	0.0301	0.2723	-119.165	11.796	-61.039
72	4.5196	-4.3561	12.8589	4.3173	-12.5592	36.8368	0.8738	-0.029	-0.7192	-0.3014	0.4462	0.4057	1.3604	-0.2577	-1.3201	1.0812	0.3904	-0.7341	0.6502	-0.0609	1.8465	-120.692	4.467	-51.353

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 124
2	X-RAY DIFFRACTION	2	A	125 - 136
3	X-RAY DIFFRACTION	3	A	137 - 195
4	X-RAY DIFFRACTION	4	A	196 - 333
5	X-RAY DIFFRACTION	5	A	334 - 381
6	X-RAY DIFFRACTION	6	A	382 - 401
7	X-RAY DIFFRACTION	7	B	28 - 54
8	X-RAY DIFFRACTION	8	B	55 - 114
9	X-RAY DIFFRACTION	9	B	115 - 131
10	X-RAY DIFFRACTION	10	B	132 - 176
11	X-RAY DIFFRACTION	11	B	177 - 209
12	X-RAY DIFFRACTION	12	B	210 - 220
13	X-RAY DIFFRACTION	13	C	26 - 125
14	X-RAY DIFFRACTION	14	C	126 - 152
15	X-RAY DIFFRACTION	15	C	153 - 177
16	X-RAY DIFFRACTION	16	C	178 - 198
17	X-RAY DIFFRACTION	17	C	199 - 370
18	X-RAY DIFFRACTION	18	C	371 - 401
19	X-RAY DIFFRACTION	19	D	28 - 54
20	X-RAY DIFFRACTION	20	D	55 - 68
21	X-RAY DIFFRACTION	21	D	69 - 86
22	X-RAY DIFFRACTION	22	D	87 - 129
23	X-RAY DIFFRACTION	23	D	130 - 188
24	X-RAY DIFFRACTION	24	D	189 - 220
25	X-RAY DIFFRACTION	25	E	26 - 65
26	X-RAY DIFFRACTION	26	E	66 - 157
27	X-RAY DIFFRACTION	27	E	158 - 204
28	X-RAY DIFFRACTION	28	E	205 - 354
29	X-RAY DIFFRACTION	29	E	355 - 381
30	X-RAY DIFFRACTION	30	E	382 - 401
31	X-RAY DIFFRACTION	31	F	28 - 53
32	X-RAY DIFFRACTION	32	F	54 - 86
33	X-RAY DIFFRACTION	33	F	87 - 142
34	X-RAY DIFFRACTION	34	F	143 - 154
35	X-RAY DIFFRACTION	35	F	155 - 209
36	X-RAY DIFFRACTION	36	F	210 - 220
37	X-RAY DIFFRACTION	37	G	26 - 118
38	X-RAY DIFFRACTION	38	G	119 - 147
39	X-RAY DIFFRACTION	39	G	148 - 187
40	X-RAY DIFFRACTION	40	G	188 - 333
41	X-RAY DIFFRACTION	41	G	334 - 375
42	X-RAY DIFFRACTION	42	G	376 - 399
43	X-RAY DIFFRACTION	43	H	28 - 54
44	X-RAY DIFFRACTION	44	H	55 - 68
45	X-RAY DIFFRACTION	45	H	69 - 86
46	X-RAY DIFFRACTION	46	H	87 - 189
47	X-RAY DIFFRACTION	47	H	190 - 213
48	X-RAY DIFFRACTION	48	H	214 - 220
49	X-RAY DIFFRACTION	49	I	26 - 70
50	X-RAY DIFFRACTION	50	I	71 - 152
51	X-RAY DIFFRACTION	51	I	153 - 193
52	X-RAY DIFFRACTION	52	I	194 - 321
53	X-RAY DIFFRACTION	53	I	322 - 382
54	X-RAY DIFFRACTION	54	I	383 - 401
55	X-RAY DIFFRACTION	55	J	28 - 50
56	X-RAY DIFFRACTION	56	J	51 - 60
57	X-RAY DIFFRACTION	57	J	61 - 76
58	X-RAY DIFFRACTION	58	J	77 - 145
59	X-RAY DIFFRACTION	59	J	146 - 209
60	X-RAY DIFFRACTION	60	J	210 - 220
61	X-RAY DIFFRACTION	61	K	26 - 59
62	X-RAY DIFFRACTION	62	K	60 - 125
63	X-RAY DIFFRACTION	63	K	126 - 157
64	X-RAY DIFFRACTION	64	K	158 - 186
65	X-RAY DIFFRACTION	65	K	187 - 264
66	X-RAY DIFFRACTION	66	K	265 - 400
67	X-RAY DIFFRACTION	67	L	28 - 45
68	X-RAY DIFFRACTION	68	L	46 - 54
69	X-RAY DIFFRACTION	69	L	55 - 87
70	X-RAY DIFFRACTION	70	L	88 - 143
71	X-RAY DIFFRACTION	71	L	144 - 214
72	X-RAY DIFFRACTION	72	L	215 - 220

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi