PDB-8rky: X-ray structure of the drug binding domain of AlbA in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 8rky

Title

X-ray structure of the drug binding domain of AlbA in complex with the KMR-14-14 compound of the pyrrolobenzodiazepines class

Components

Albicidin resistance protein

Keywords

DNA BINDING PROTEIN / DRUG BINDING / BACTERIAL RESISTANCE / PYRROLOBENZODIAZEPINES

Function / homology

TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / : / : / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Albicidin resistance protein

Function and homology information

Biological species

Klebsiella oxytoca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.17 Å

Authors

Di Palma, M. / Surani, Y.M. / Rahman, K.M. / Steiner, R.A.

Funding support

United Kingdom,

Italy, 2items

Citation

Journal: To Be Published
Title: X-ray structure of the drug binding domain of AlbA in complex with the KMR-14-14 compound of the pyrrolobenzodiazepines class
Authors: Di Palma, M. / Surani, Y.M. / Rahman, K.M. / Steiner, R.A.

History

Deposition	Jan 1, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8rky.cif.gz	289.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8rky.ent.gz		Display	PDB format
PDBx/mmJSON format	8rky.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rk/8rky ftp://data.pdbj.org/pub/pdb/validation_reports/rk/8rky	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

BBB: Albicidin resistance protein

CCC: Albicidin resistance protein

AAA: Albicidin resistance protein

hetero molecules

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

1

BBB: Albicidin resistance protein

hetero molecules

defined by author
Evidence: gel filtration
27.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: Albicidin resistance protein

hetero molecules

defined by author
27.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

AAA: Albicidin resistance protein

hetero molecules

defined by author
28 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	182.631, 118.950, 57.702
Angle α, β, γ (deg.)	90.000, 92.073, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	BBB
2	1	CCC
3	2	BBB
4	2	AAA
5	3	CCC
6	3	AAA

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	BBB	A	0 - 216	1 - 217
2	2	1	CCC	B	0 - 216	1 - 217
3	1	2	BBB	A	0 - 214	1 - 215
4	2	2	AAA	C	0 - 214	1 - 215
5	1	3	CCC	B	0 - 214	1 - 215
6	2	3	AAA	C	0 - 214	1 - 215

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Albicidin resistance protein Mass: 26081.402 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: albA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KRS7
#2: Chemical	ChemComp-A1H1R / ethyl 4-[[5-[[4-[4-[[(6~{a}~{S})-2-methoxy-11-oxidanylidene-6~{a},7,8,9-tetrahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-benzothiophen-2-yl]carbonylamino]-1-methyl-imidazole-2-carboxylate Mass: 780.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₉H₄₀N₈O₈S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1H1Q / ~{S}-[(2~{S},3~{S})-2,3-bis(oxidanyl)-4-sulfanyl-butyl] 4-[[5-[[4-[4-[[(6~{a}~{S})-2-methoxy-11-oxidanylidene-6~{a},7,8,9-tetrahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-benzothiophen-2-yl]carbonylamino]-1-methyl-imidazole-2-carbothioate Mass: 889.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₁H₄₄N₈O₉S₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4 Å³/Da / Density % sol: 69.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.2M Ammonium sulphate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 2.17→49.49 Å / Num. obs: 64940 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_pim(I) all: 0.03 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.17→2.25 Å / Redundancy: 4.4 % / R_merge(I) obs: 1.435 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6345 / CC_1/2: 0.365 / R_pim(I) all: 0.764 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.17→49.49 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.955 / SU B: 12.301 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2337	3278	5.05 %
R_work	0.2084	61627	-
all	0.21	-	-
obs	-	64905	99.745 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 68.747 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.489 Å²	-0 Å²	-0.421 Å²
2-	-	-0.365 Å²	-0 Å²
3-	-	-	-0.093 Å²

Refinement step

Cycle: LAST / Resolution: 2.17→49.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5358	0	370	226	5954

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	6040
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.015	5453
X-RAY DIFFRACTION	r_angle_refined_deg	1.273	1.656	8211
X-RAY DIFFRACTION	r_angle_other_deg	1.187	1.638	12487
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.692	5	674
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.335	21.763	380
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.23	15	993
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.761	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	701
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	7633
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1549
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1331
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	4955
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	2913
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2570
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	217
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.022	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.225	0.2	33
X-RAY DIFFRACTION	r_nbd_other	0.173	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.176	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.722	4.714	2666
X-RAY DIFFRACTION	r_mcbond_other	1.722	4.713	2665
X-RAY DIFFRACTION	r_mcangle_it	2.863	7.058	3350
X-RAY DIFFRACTION	r_mcangle_other	2.862	7.06	3351
X-RAY DIFFRACTION	r_scbond_it	2.309	5.593	3374
X-RAY DIFFRACTION	r_scbond_other	2.309	5.594	3375
X-RAY DIFFRACTION	r_scangle_it	3.893	8.279	4861
X-RAY DIFFRACTION	r_scangle_other	3.892	8.281	4862
X-RAY DIFFRACTION	r_lrange_it	9.317	58.231	6928
X-RAY DIFFRACTION	r_lrange_other	9.339	58.043	6879
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.096	0.05	7167
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.085	0.05	7179
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.09	0.05	7179

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	BBB	X-RAY DIFFRACTION	Local ncs	0.09611	0.05008
1	2	CCC	X-RAY DIFFRACTION	Local ncs	0.09611	0.05008
2	3	BBB	X-RAY DIFFRACTION	Local ncs	0.08469	0.05008
2	4	AAA	X-RAY DIFFRACTION	Local ncs	0.08469	0.05008
3	5	CCC	X-RAY DIFFRACTION	Local ncs	0.08976	0.05008
3	6	AAA	X-RAY DIFFRACTION	Local ncs	0.08976	0.05008

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 (%)
2.17-2.226	0.373	251	0.367	4533	X-RAY DIFFRACTION	99.4388
2.226-2.287	0.346	221	0.337	4397	X-RAY DIFFRACTION	99.6978
2.287-2.354	0.309	223	0.312	4322	X-RAY DIFFRACTION	99.978
2.354-2.426	0.315	220	0.284	4203	X-RAY DIFFRACTION	99.9774
2.426-2.506	0.283	225	0.267	4055	X-RAY DIFFRACTION	99.9766
2.506-2.593	0.284	213	0.249	3947	X-RAY DIFFRACTION	99.7841
2.593-2.691	0.3	214	0.24	3760	X-RAY DIFFRACTION	99.9246
2.691-2.801	0.237	201	0.231	3656	X-RAY DIFFRACTION	99.9482
2.801-2.925	0.282	204	0.235	3455	X-RAY DIFFRACTION	99.9727
2.925-3.068	0.277	200	0.228	3353	X-RAY DIFFRACTION	100
3.068-3.234	0.313	141	0.246	3224	X-RAY DIFFRACTION	99.9703
3.234-3.43	0.255	158	0.233	3011	X-RAY DIFFRACTION	99.9054
3.43-3.666	0.232	157	0.215	2830	X-RAY DIFFRACTION	99.5003
3.666-3.96	0.235	124	0.186	2630	X-RAY DIFFRACTION	99.6382
3.96-4.337	0.171	131	0.171	2446	X-RAY DIFFRACTION	99.383
4.337-4.848	0.203	119	0.164	2188	X-RAY DIFFRACTION	99.2685
4.848-5.595	0.223	77	0.187	1963	X-RAY DIFFRACTION	99.2218
5.595-6.848	0.21	86	0.193	1652	X-RAY DIFFRACTION	99.5418
6.848-9.661	0.165	85	0.153	1278	X-RAY DIFFRACTION	99.8535
9.661-49.49	0.181	28	0.177	724	X-RAY DIFFRACTION	97.5357

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	8.0306	-4.1962	2.846	15.815	-12.8778	10.5545	0.8294	1.1966	0.7045	-1.897	-0.1276	0.7791	1.4236	0.0292	-0.7018	0.6866	0.0582	-0.0232	0.4113	0.2676	0.3243	3.0263	-7.7943	-18.6245
2	2.9489	-2.0034	-6.4878	13.3906	2.1597	14.7357	-0.1166	0.2822	-0.0599	-1.277	0.096	0.7993	0.5463	-0.5303	0.0206	0.2147	0.096	0.033	0.5359	0.1592	0.3992	12.3943	-9.8803	-18.9452
3	1.7761	0.4981	-0.7793	8.0078	-4.919	6.7257	-0.082	0.1507	0.0813	-0.1894	-0.0858	-0.0931	0.2356	-0.0457	0.1678	0.0482	0.0356	0.0348	0.1783	-0.0382	0.1466	19.0425	-24.3781	-12.5666
4	3.0658	-0.7714	1.0665	3.4944	0.9931	8.7203	-0.0407	-0.0744	-0.1806	0.1797	-0.1775	-0.3956	0.3675	0.376	0.2182	0.0307	0.0444	-0.0063	0.179	0.031	0.1813	22.556	-25.1665	-0.3245
5	12.2399	-6.6471	-1.2225	7.5407	-2.2557	7.0952	-0.0529	0.1772	1.7007	0.3484	0.2358	-0.8384	-1.0228	-0.0343	-0.1829	0.2131	0.0578	0.021	0.1265	0.0706	0.2542	14.4174	-10.1143	-8.5078
6	6.4088	5.1026	0.0847	11.1398	5.6335	4.4741	-0.0697	0.6195	0.4425	-0.2592	0.1879	0.2634	-0.0355	-0.0865	-0.1182	0.1723	0.1923	-0.0752	0.3216	0.015	0.1539	3.6387	-16.5696	-11.7878
7	5.5958	0.6556	6.5214	3.4163	1.8335	8.4211	0.1129	-0.1167	0.0562	-0.6119	-0.4207	0.3865	0.0076	-0.5729	0.3078	0.1487	0.0153	-0.0164	0.36	-0.0609	0.2077	7.7293	-24.1503	-14.1662
8	4.2852	1.7664	7.5232	1.5399	4.3348	15.096	0.5096	-0.0248	-0.2843	0.1633	-0.3447	0.114	0.8247	-0.5991	-0.1649	0.0798	0.0093	-0.0069	0.307	-0.0399	0.2146	10.8856	-25.4912	-4.2098
9	2.4829	0.9112	4.7539	2.2133	1.64	11.1347	-0.0388	0.1066	0.0174	0.0149	-0.0278	0.0525	-0.2577	-0.0454	0.0666	0.0184	0.0212	0.0005	0.04	-0.0017	0.0113	19.6242	-18.0097	9.4977
10	9.8298	-2.0767	3.2822	5.3518	-2.6834	2.1342	0.3061	-0.0132	0.0172	-0.3793	-0.1408	0.3022	0.3989	-0.102	-0.1653	0.1621	-0.1051	-0.0146	0.1094	0.0204	0.1965	10.5405	-17.1073	12.1832
11	5.8129	-5.2263	0.5005	13.3902	-11.7541	14.8669	0.164	0.0929	0.3237	-0.2861	0.4769	0.1575	-0.0743	-0.7016	-0.6409	0.5829	-0.0753	0.0631	0.1602	0.091	0.4966	8.0091	-3.9785	1.8387
12	11.2493	-7.6058	-5.7555	5.1472	3.9898	5.9577	0.0095	0.2203	-0.6561	-0.0383	-0.1387	0.4155	-0.7289	-0.115	0.1291	0.5433	-0.0186	0.0033	0.391	0.079	0.5772	9.1473	6.1164	-3.3989
13	6.6124	2.1932	-2.2074	5.8272	-0.676	0.7681	-0.2765	0.4768	-0.0198	-0.0151	0.1784	-0.2052	0.005	-0.2241	0.0981	0.4891	0.1435	-0.0771	0.3885	-0.1102	0.5276	10.8755	11.7758	2.9276
14	0.3041	-0.1108	-0.5684	0.049	0.2305	1.1293	-0.0551	0.1754	-0.0121	-0.018	-0.0772	0.0508	-0.0214	-0.3618	0.1324	0.3494	0.0631	-0.024	0.2142	0.0255	0.4852	5.5901	7.3859	8.548
15	8.9614	-3.4082	3.2122	8.3641	-1.3227	7.6188	-0.0484	-0.6548	0.5319	0.4343	0.162	0.9426	-0.5982	-0.3636	-0.1136	0.083	0.0156	0.1268	0.0559	-0.0188	0.4168	9.6388	-5.7987	15.0256
16	9.6507	1.3016	-1.9985	6.3338	3.5808	8.0449	-0.0472	-0.1864	0.658	-0.2939	0.1763	0.1239	-0.6766	0.4535	-0.1291	0.0676	-0.0407	0.0173	0.0299	-0.0306	0.1345	22.3227	-6.2731	15.1506
17	12.3565	0.6734	10.5507	3.1034	-1.2271	10.0771	-0.1472	0.4682	0.1873	-0.4421	0.1101	0.1513	0.0896	0.3481	0.0371	0.2961	-0.0379	0.0914	0.2024	0.0425	0.2312	23.6846	-9.9396	2.7974
18	0.0092	-0.2494	-0.1757	11.0482	7.7009	5.3696	0.0192	0.0236	0.0236	-0.0684	-0.006	-0.023	-0.0639	-0.0169	-0.0133	0.3481	-0.0677	0.105	0.3296	0.0194	0.5123	16.6631	-0.6385	1.7207
19	9.7076	-1.1157	-4.5111	6.1923	-0.635	2.8878	0.1364	-0.2953	0.0867	-0.0892	-0.1043	-0.1593	-0.075	0.2287	-0.0321	0.2628	-0.0073	0.0328	0.2259	-0.0098	0.2782	14.4684	5.1204	13.0684
20	14.7284	-0.3251	-4.0006	8.9793	-6.6406	6.1441	0.0171	0.2503	-0.1807	-0.718	-0.1586	-0.0396	0.5154	0.0591	0.1415	0.3742	-0.0615	-0.0203	0.3785	-0.0069	0.3611	12.2136	9.5012	19.2774
21	4.6778	-0.4847	2.0099	6.6133	4.0473	5.0781	-0.0563	-0.3123	-0.0844	0.3775	0.0838	-0.1531	0.0953	-0.2188	-0.0275	0.2506	0.0765	0.0326	0.213	0.0062	0.0984	44.8355	-47.4118	-7.4439
22	1.738	-1.1298	-2.2881	2.4806	-0.5461	5.4377	-0.1461	-0.1079	-0.1027	0.2748	-0.0604	-0.0304	0.0225	0.1367	0.2065	0.4931	-0.0312	-0.0547	0.4818	0.0743	0.218	37.7594	-41.9094	-3.3491
23	1.6315	-3.1383	5.1521	6.2981	-10.4368	17.3455	0.1981	-0.2674	-0.116	-0.2692	0.1023	0.1749	0.4529	0.0051	-0.3004	0.4602	-0.0735	0.0664	0.7404	0.1226	0.2727	27.9857	-39.8253	-3.0735
24	5.6835	1.0774	4.6793	0.8596	2.8785	10.922	-0.1498	0.0475	-0.2212	-0.0192	-0.0043	0.1611	0.1934	-0.3387	0.1541	0.2948	-0.0644	0.0459	0.1802	0.0523	0.2593	18.415	-40.9331	-16.2776
25	10.3356	-3.2192	5.0636	6.6279	-1.7518	9.5499	-0.3611	0.0294	0.1738	0.0133	-0.009	0.4233	0.4358	-0.4943	0.3701	0.1451	-0.015	0.0858	0.0991	0.0009	0.1279	22.1551	-32.418	-19.2451
26	17.8589	1.6384	-0.8402	4.5963	-0.9545	4.9884	-0.0834	-0.4273	0.185	0.1276	0.0247	-0.1745	-0.1567	0.2146	0.0586	0.1772	0.062	0.0204	0.1475	-0.0095	0.1302	37.2379	-34.914	-10.0899
27	3.2974	2.928	1.2755	8.4922	1.2286	3.9386	0.0156	-0.1033	-0.058	0.3379	-0.0695	-0.0177	-0.1949	0.3185	0.0539	0.1742	0.0772	0.0604	0.1474	-0.0093	0.1272	39.7348	-44.0351	-16.2323
28	2.2015	-2.274	-2.5612	7.6989	3.6468	3.2219	0.0081	0.0105	-0.2694	0.3789	-0.1212	-0.1763	-0.0123	-0.0682	0.1131	0.2677	0.0399	0.0567	0.2692	0.0331	0.3582	31.307	-52.1636	-12.4918
29	0.3698	0.7544	0.1671	10.1434	-8.0902	10.3207	0.0541	0.0778	-0.0264	0.161	-0.04	0.485	0.6056	0.1494	-0.0141	0.2095	-0.0057	0.1678	0.0644	-0.0313	0.1771	27.6414	-30.3443	-26.6167
30	2.338	-0.9105	2.1601	7.0828	-1.3346	11.9074	0.0954	0.2047	-0.1448	-0.6411	-0.073	-0.2612	0.0804	-0.1754	-0.0224	0.0808	-0.016	0.0037	0.1752	-0.0526	0.0832	31.5794	-28.733	-36.4733
31	8.369	-1.034	7.6416	2.3214	-0.0028	12.7686	0.449	-0.286	-0.4048	0.5386	-0.1758	-0.132	0.8126	-0.0026	-0.2733	0.2374	-0.0219	-0.0402	0.108	0.0089	0.206	42.1649	-32.8537	-25.332
32	3.5753	0.4817	-2.2824	14.8654	-1.0423	7.1611	0.0221	-0.2604	0.1593	0.2019	0.0811	-0.0468	0.1449	-0.0286	-0.1033	0.2885	-0.0189	-0.0242	0.3101	-0.0376	0.2913	53.6305	-27.3685	-12.8246
33	6.7311	0.8424	-1.92	0.3313	0.7869	5.437	-0.3182	0.0452	-0.1423	0.0262	0.1005	0.0466	0.2446	0.6029	0.2176	0.2557	-0.0012	0.0117	0.3651	-0.015	0.3359	58.5734	-22.0083	-20.4149
34	5.8016	3.0444	3.7199	1.7628	2.0698	2.4865	-0.0179	0.1648	-0.0403	0.0545	0.1692	-0.2437	0.0368	0.2294	-0.1513	0.1632	0.0124	-0.0478	0.2936	0.0039	0.3705	52.8568	-25.9118	-26.5142
35	6.9114	0.0102	7.7937	7.0182	-1.0204	8.947	0.0736	0.2958	-0.2266	0.0804	0.0819	-0.6535	0.0519	0.2947	-0.1555	0.0455	0.0668	0.0259	0.1296	-0.0045	0.156	42.4739	-25.7099	-33.5456
36	4.9377	-0.7356	-3.676	9.6284	-1.1434	3.0444	0.0939	-0.11	-0.1284	0.0219	-0.2051	-0.1781	-0.0956	0.1457	0.1113	0.092	-0.0729	-0.0017	0.1396	-0.0228	0.1397	38.119	-15.4124	-32.0697
37	0.9846	2.5827	-0.463	11.1125	-7.7519	10.1782	0.1648	-0.018	-0.1528	0.448	-0.1101	-0.3741	-0.0273	0.1882	-0.0547	0.2104	0.0054	-0.0027	0.1659	-0.0341	0.1898	33.3711	-18.1035	-20.7952
38	3.3425	-2.6927	-4.8701	8.2969	1.0086	8.5487	0.3558	-0.2321	0.6884	-0.2626	0.5729	-0.5011	-0.5581	0.252	-0.9286	0.3537	0.051	-0.0306	0.2309	0.0755	0.3053	37.1383	-27.6143	-16.2176
39	3.1721	-0.0583	-1.2982	2.7525	-1.1005	7.0415	-0.0828	-0.0494	0.0355	0.0348	-0.153	0.0708	-0.0664	0.2409	0.2358	0.2005	-0.0295	-0.0225	0.2217	-0.0016	0.2821	48.8076	-18.3567	-22.1736
40	29.7895	-14.5703	0.867	14.2856	0.3041	0.1078	-0.343	-0.6951	-0.5782	0.323	0.4013	0.4322	0.0054	-0.0337	-0.0582	0.4044	-0.0014	-0.0132	0.3542	0.0464	0.4279	55.4003	-13.3114	-33.4911
41	4.3626	0.1605	-2.1202	0.013	-0.1472	2.7971	-0.2029	-0.3012	0.1302	0.0261	0.0062	-0.0257	0.1003	-0.1455	0.1967	0.3666	0.0113	-0.0566	0.244	-0.0424	0.3041	49.2999	26.3082	-14.507
42	2.9875	2.9468	-2.0653	5.5513	-0.8905	6.0852	0.0187	-0.1979	0.2971	0.1229	0.2044	0.1421	0.23	-0.0901	-0.2231	0.271	-0.0066	0.0252	0.2696	-0.0315	0.251	39.28	25.6134	-14.8837
43	2.7268	-0.7343	0.3845	9.3501	-4.1867	3.5624	-0.0634	-0.0145	0.0575	-0.2786	0.2169	0.3374	0.0404	0.0481	-0.1535	0.3033	0.0074	0.0302	0.3246	0.0006	0.2809	39.2745	15.4496	-4.9446
44	14.48	-2.3107	-3.2702	4.5208	1.8095	11.2973	-0.1713	-1.0808	-0.2021	0.82	0.1207	0.0962	-0.1474	-0.1076	0.0506	0.4578	-0.002	-0.0078	0.3657	0.0093	0.0835	45.6511	5.6099	-8.3092
45	0.4769	0.3281	-1.4532	6.6594	1.453	7.3528	-0.1358	0.1223	-0.1384	0.2169	0.2446	-0.2884	0.2677	0.2207	-0.1088	0.2955	-0.0246	-0.0048	0.3508	-0.0461	0.3489	54.9255	-3.4204	-13.5025
46	10.3224	-5.6149	2.015	3.2399	-1.2274	0.487	0.0509	-0.5018	-0.2854	-0.1123	0.0226	0.1641	0.0776	0.0767	-0.0735	0.3544	0.0224	0.0358	0.3872	-0.0048	0.301	48.4003	-7.6082	-19.1861
47	4.3465	-1.8431	-1.8792	9.9128	-0.6652	1.1254	-0.1747	-0.288	-0.0262	0.0157	0.2387	0.3425	0.0438	-0.0226	-0.064	0.257	-0.026	0.0123	0.2845	0.0231	0.0633	41.3389	4.8653	-17.0541
48	8.4355	4.705	-1.6943	5.7516	-3.7889	3.1223	0.1245	0.0172	0.6228	0.2413	-0.0543	0.4573	-0.3235	-0.0604	-0.0702	0.2831	0.0301	0.001	0.2488	-0.0583	0.2535	38.2945	19.3899	-21.6492
49	6.8773	0.6919	3.6615	0.4204	-0.0952	2.9733	0.0487	-0.4206	0.1797	0.1967	-0.0762	-0.0435	0.0147	-0.0554	0.0276	0.3199	-0.0051	-0.0465	0.1795	-0.0403	0.2127	51.1255	19.0702	-18.3087
50	6.604	3.7099	5.8105	9.2307	7.2465	8.5211	0.0401	-0.3897	-0.0171	0.4763	0.1704	-0.4892	-0.271	0.1704	-0.2105	0.3466	-0.1464	-0.0258	0.1608	-0.0135	0.0703	47.1357	2.3895	-23.6628
51	2.7933	0.5243	0.7948	10.2941	0.8701	1.0977	0.049	0.0001	-0.3152	0.0174	-0.0834	-0.4355	0.0164	0.1083	0.0344	0.1002	-0.0571	0.0567	0.1625	0.0103	0.1394	47.4632	-0.5026	-37.4396
52	5.2831	-4.9733	-7.9975	12.8891	4.7159	13.195	-0.0022	-0.1124	0.3656	0.2878	0.4719	-0.0689	-0.1665	-0.0872	-0.4697	0.2197	-0.0151	-0.0756	0.3199	-0.1281	0.3363	39.7892	16.1692	-31.8028
53	1.0508	1.102	-1.4345	8.1924	4.4952	8.0246	-0.0818	0.3179	-0.1987	-0.1276	0.017	-0.0194	-0.181	-0.379	0.0648	0.3008	-0.0141	0.0148	0.5118	0.0173	0.4877	26.971	23.3327	-30.6976
54	6.0813	-3.3513	0.3178	1.9189	-0.2698	0.1755	0.1136	0.164	0.4091	0.0009	-0.0259	-0.0989	-0.1292	-0.1443	-0.0876	0.2861	0.023	0.002	0.3238	0.0412	0.3502	33.4893	17.9948	-41.2671
55	12.1234	4.9944	-0.361	5.5331	-0.1576	2.2293	-0.1237	0.5853	0.3197	-0.4202	0.087	0.3217	-0.294	-0.1596	0.0366	0.1803	-0.0524	-0.0121	0.1124	-0.0068	0.0466	36.7345	1.02	-41.7592
56	1.7162	2.0525	1.4012	4.8389	0.8877	5.5172	-0.0231	-0.3793	-0.0906	0.2932	-0.168	0.104	-0.0893	-0.2025	0.1911	0.1357	0.0032	0.0527	0.2329	-0.0062	0.2022	30.7626	-1.5598	-29.8037
57	0.8626	-0.3747	0.2265	7.4349	2.7763	4.0319	-0.0381	0.3258	-0.1437	0.1266	0.2731	0.4668	0.0454	-0.2695	-0.235	0.2086	-0.0515	0.0436	0.2547	0.0001	0.2559	34.8286	8.2742	-25.5005
58	6.7921	-1.5357	-4.8684	5.7337	-7.0981	16.0818	0.2095	0.5466	-0.1363	0.0097	-0.285	0.0411	-0.1603	-0.3717	0.0755	0.2149	-0.0679	-0.04	0.5488	0.065	0.4083	27.8822	12.3455	-33.2112
59	3.7723	1.0112	4.7871	11.2611	-4.2704	8.8848	0.0092	0.1295	-0.0129	0.1822	-0.1026	-0.204	-0.0986	0.1984	0.0935	0.2875	0.0214	-0.0484	0.5921	0.0482	0.2763	28.3133	12.081	-43.5644
60	9.5363	5.85	0.6827	8.7895	-3.6234	3.1916	0.4016	-0.0266	-0.0805	-0.068	0.0633	0.5205	0.2743	-0.073	-0.465	0.3424	0.0089	0.0039	0.3518	0.036	0.3545	26.8537	12.272	-51.9699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	0 - 13
2	X-RAY DIFFRACTION	2	ALL	AAA	14 - 19
3	X-RAY DIFFRACTION	3	ALL	AAA	20 - 41
4	X-RAY DIFFRACTION	4	ALL	AAA	42 - 55
5	X-RAY DIFFRACTION	5	ALL	AAA	56 - 70
6	X-RAY DIFFRACTION	6	ALL	AAA	71 - 84
7	X-RAY DIFFRACTION	7	ALL	AAA	85 - 92
8	X-RAY DIFFRACTION	8	ALL	AAA	93 - 97
9	X-RAY DIFFRACTION	9	ALL	AAA	98 - 117
10	X-RAY DIFFRACTION	10	ALL	AAA	118 - 131
11	X-RAY DIFFRACTION	11	ALL	AAA	132 - 141
12	X-RAY DIFFRACTION	12	ALL	AAA	142 - 146
13	X-RAY DIFFRACTION	13	ALL	AAA	147 - 151
14	X-RAY DIFFRACTION	14	ALL	AAA	152 - 159
15	X-RAY DIFFRACTION	15	ALL	AAA	160 - 175
16	X-RAY DIFFRACTION	16	ALL	AAA	176 - 187
17	X-RAY DIFFRACTION	17	ALL	AAA	188 - 193
18	X-RAY DIFFRACTION	18	ALL	AAA	194 - 204
19	X-RAY DIFFRACTION	19	ALL	AAA	205 - 212
20	X-RAY DIFFRACTION	20	ALL	AAA	213 - 215
21	X-RAY DIFFRACTION	21	ALL	BBB	0 - 13
22	X-RAY DIFFRACTION	22	ALL	BBB	14 - 19
23	X-RAY DIFFRACTION	23	ALL	BBB	20 - 27
24	X-RAY DIFFRACTION	24	ALL	BBB	28 - 41
25	X-RAY DIFFRACTION	25	ALL	BBB	42 - 58
26	X-RAY DIFFRACTION	26	ALL	BBB	59 - 67
27	X-RAY DIFFRACTION	27	ALL	BBB	68 - 81
28	X-RAY DIFFRACTION	28	ALL	BBB	82 - 88
29	X-RAY DIFFRACTION	29	ALL	BBB	89 - 120
30	X-RAY DIFFRACTION	30	ALL	BBB	121 - 125
31	X-RAY DIFFRACTION	31	ALL	BBB	126 - 141
32	X-RAY DIFFRACTION	32	ALL	BBB	142 - 147
33	X-RAY DIFFRACTION	33	ALL	BBB	148 - 153
34	X-RAY DIFFRACTION	34	ALL	BBB	154 - 162
35	X-RAY DIFFRACTION	35	ALL	BBB	163 - 172
36	X-RAY DIFFRACTION	36	ALL	BBB	173 - 182
37	X-RAY DIFFRACTION	37	ALL	BBB	183 - 191
38	X-RAY DIFFRACTION	38	ALL	BBB	192 - 197
39	X-RAY DIFFRACTION	39	ALL	BBB	198 - 213
40	X-RAY DIFFRACTION	40	ALL	BBB	214 - 216
41	X-RAY DIFFRACTION	41	ALL	CCC	0 - 6
42	X-RAY DIFFRACTION	42	ALL	CCC	7 - 17
43	X-RAY DIFFRACTION	43	ALL	CCC	18 - 24
44	X-RAY DIFFRACTION	44	ALL	CCC	25 - 34
45	X-RAY DIFFRACTION	45	ALL	CCC	35 - 42
46	X-RAY DIFFRACTION	46	ALL	CCC	43 - 48
47	X-RAY DIFFRACTION	47	ALL	CCC	49 - 63
48	X-RAY DIFFRACTION	48	ALL	CCC	64 - 70
49	X-RAY DIFFRACTION	49	ALL	CCC	71 - 84
50	X-RAY DIFFRACTION	50	ALL	CCC	85 - 115
51	X-RAY DIFFRACTION	51	ALL	CCC	116 - 129
52	X-RAY DIFFRACTION	52	ALL	CCC	130 - 142
53	X-RAY DIFFRACTION	53	ALL	CCC	143 - 147
54	X-RAY DIFFRACTION	54	ALL	CCC	148 - 165
55	X-RAY DIFFRACTION	55	ALL	CCC	166 - 184
56	X-RAY DIFFRACTION	56	ALL	CCC	185 - 190
57	X-RAY DIFFRACTION	57	ALL	CCC	191 - 197
58	X-RAY DIFFRACTION	58	ALL	CCC	198 - 205
59	X-RAY DIFFRACTION	59	ALL	CCC	206 - 212
60	X-RAY DIFFRACTION	60	ALL	CCC	213 - 216

-
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