PDB-9dsz: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne...

ID or keywords:

Entry

Database: PDB / ID: 9dsz

Title

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (DTP bound)

Components

ADP-ribose pyrophosphatase

Keywords

HYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ADP-ribose diphosphatase

Function / homology

Function and homology information

ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (DTP bound)
Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.

History

Deposition	Sep 30, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9dsz.cif.gz	661.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9dsz.ent.gz	547.8 KB	Display	PDB format
PDBx/mmJSON format	9dsz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9dsz_validation.pdf.gz	6.5 MB	Display	wwPDB validaton report
Full document	9dsz_full_validation.pdf.gz	6.6 MB	Display
Data in XML	9dsz_validation.xml.gz	74.5 KB	Display
Data in CIF	9dsz_validation.cif.gz	94.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/9dsz ftp://data.pdbj.org/pub/pdb/validation_reports/ds/9dsz	HTTPS FTP

-
Related structure data

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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (6) #201 - Sep 2016 Isoprene Synthase similarity (4) #177 - Sep 2014 Apoptosomes similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: ADP-ribose pyrophosphatase

B: ADP-ribose pyrophosphatase

C: ADP-ribose pyrophosphatase

D: ADP-ribose pyrophosphatase

E: ADP-ribose pyrophosphatase

F: ADP-ribose pyrophosphatase

G: ADP-ribose pyrophosphatase

H: ADP-ribose pyrophosphatase

hetero molecules

202 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ADP-ribose pyrophosphatase

B: ADP-ribose pyrophosphatase

hetero molecules

defined by author&software
Evidence: gel filtration
50.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ADP-ribose pyrophosphatase

D: ADP-ribose pyrophosphatase

hetero molecules

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

3

E: ADP-ribose pyrophosphatase

F: ADP-ribose pyrophosphatase

hetero molecules

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

4

G: ADP-ribose pyrophosphatase

H: ADP-ribose pyrophosphatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.843, 79.311, 115.827
Angle α, β, γ (deg.)	90.00, 90.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ADP-ribose pyrophosphatase / ADP-ribose diphosphatase / ADP-ribose phosphohydrolase / Adenosine diphosphoribose pyrophosphatase Mass: 24742.848 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: HS11286 / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPHS_45750 / Plasmid: KlpnC.20447.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GVQ7, ADP-ribose diphosphatase
#2: Chemical	ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.15 Å³/Da / Density % sol: 42.91 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.5, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 AB/12. 5 hour soak in 5mM DTP/MgCl2, Puck: PSL-0206, Cryo: 30% (v/v) PEG 3350, ...Details: 20% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.5, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 AB/12. 5 hour soak in 5mM DTP/MgCl2, Puck: PSL-0206, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.5.

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.91 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.5, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 AB/12. 5 hour soak in 5mM DTP/MgCl2, Puck: PSL-0206, Cryo: 30% (v/v) PEG 3350, ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.9→92.84 Å / Num. obs: 132200 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.097 / R_pim(I) all: 0.043 / R_rim(I) all: 0.106 / Χ²: 1 / Net I/σ(I): 10 / Num. measured all: 781765
Reflection shell	Resolution: 1.9→1.95 Å / % possible obs: 99.7 % / Redundancy: 5.9 % / R_merge(I) obs: 1.256 / Num. measured all: 57372 / Num. unique obs: 9727 / CC_1/2: 0.695 / R_pim(I) all: 0.556 / R_rim(I) all: 1.377 / Χ²: 0.98 / Net I/σ(I) obs: 1.6

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_5396: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→72.63 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2334	6548	4.96 %
R_work	0.1962	-	-
obs	0.198	131970	99.56 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→72.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12430	0	234	679	13343

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	13046
X-RAY DIFFRACTION	f_angle_d	0.87	17759
X-RAY DIFFRACTION	f_dihedral_angle_d	14.491	4917
X-RAY DIFFRACTION	f_chiral_restr	0.061	1969
X-RAY DIFFRACTION	f_plane_restr	0.008	2272

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 (%)
1.9-1.92	0.3624	191	0.3029	4175	X-RAY DIFFRACTION	99
1.92-1.94	0.3168	211	0.2787	4158	X-RAY DIFFRACTION	99
1.94-1.97	0.3168	203	0.275	4166	X-RAY DIFFRACTION	99
1.97-1.99	0.3082	212	0.26	4135	X-RAY DIFFRACTION	100
1.99-2.02	0.2924	218	0.2533	4182	X-RAY DIFFRACTION	100
2.02-2.05	0.285	215	0.2478	4147	X-RAY DIFFRACTION	100
2.05-2.08	0.2812	226	0.2454	4187	X-RAY DIFFRACTION	100
2.08-2.11	0.2476	243	0.2358	4161	X-RAY DIFFRACTION	100
2.11-2.14	0.2951	246	0.2176	4129	X-RAY DIFFRACTION	100
2.14-2.17	0.2525	205	0.2135	4158	X-RAY DIFFRACTION	100
2.17-2.21	0.2804	231	0.2114	4189	X-RAY DIFFRACTION	100
2.21-2.25	0.2509	186	0.2086	4170	X-RAY DIFFRACTION	100
2.25-2.3	0.2519	223	0.2068	4189	X-RAY DIFFRACTION	100
2.3-2.34	0.2458	240	0.2101	4170	X-RAY DIFFRACTION	100
2.34-2.39	0.2718	208	0.2148	4207	X-RAY DIFFRACTION	100
2.39-2.45	0.2811	239	0.2075	4129	X-RAY DIFFRACTION	100
2.45-2.51	0.2574	224	0.1962	4176	X-RAY DIFFRACTION	100
2.51-2.58	0.2583	210	0.1982	4204	X-RAY DIFFRACTION	100
2.58-2.65	0.2589	231	0.2059	4185	X-RAY DIFFRACTION	100
2.65-2.74	0.301	211	0.2166	4178	X-RAY DIFFRACTION	100
2.74-2.84	0.2345	205	0.2194	4203	X-RAY DIFFRACTION	100
2.84-2.95	0.2721	205	0.2141	4168	X-RAY DIFFRACTION	100
2.95-3.09	0.2636	224	0.2116	4161	X-RAY DIFFRACTION	99
3.09-3.25	0.256	222	0.2125	4192	X-RAY DIFFRACTION	100
3.25-3.45	0.2274	230	0.1994	4200	X-RAY DIFFRACTION	99
3.45-3.72	0.1905	199	0.1806	4127	X-RAY DIFFRACTION	97
3.72-4.09	0.1775	210	0.1577	4228	X-RAY DIFFRACTION	100
4.09-4.69	0.177	250	0.1403	4209	X-RAY DIFFRACTION	100
4.69-5.9	0.1852	212	0.1558	4236	X-RAY DIFFRACTION	100
5.9-72.63	0.2136	218	0.2064	4303	X-RAY DIFFRACTION	98

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	6.1703	1.0536	-3.3098	5.2727	-1.7225	6.6065	-0.0653	0.6786	0.663	-0.527	0.1377	0.071	-0.3801	-0.1575	-0.1096	0.3488	0.0064	-0.0034	0.3445	0.0513	0.2917	3.5625	3.4505	64.2448
2	5.0246	1.2481	-1.1454	3.5091	-2.6038	5.6248	0.0275	0.3514	0.2876	-0.1444	0.3827	0.8197	0.1119	-0.5328	-0.4177	0.2751	-0.0461	0.0421	0.3901	-0.0391	0.3743	-3.2258	-5.2864	71.0882
3	7.1073	2.6562	2.2495	4.3632	1.1152	4.2329	0.1728	-0.336	0.1449	-0.0676	-0.1513	-0.0237	-0.377	0.8445	-0.0167	0.336	0.0033	-0.0123	0.7281	-0.0499	0.2962	11.3832	-0.2489	58.0429
4	2.2286	0.5535	0.5429	1.2056	0.3468	3.083	-0.0827	-0.1722	0.0685	0.3912	-0.0432	0.1588	0.1271	-0.1622	0.0508	0.2423	0.0484	0.0015	0.2263	-0.0106	0.1879	3.3265	-0.5691	84.1792
5	1.9576	1.763	2.7925	4.2485	3.1459	4.7999	0.1754	-0.7313	-0.1668	0.411	-0.1257	-0.0586	0.3597	-0.4287	-0.0146	0.4281	-0.0397	0.0315	0.5378	0.0514	0.291	6.2576	-7.3057	99.4067
6	2.3089	-0.8812	2.1676	1.7969	-1.8532	2.7815	-0.1762	0.025	0.2358	-0.0648	0.0278	1.4002	-0.3268	-1.0397	0.138	0.5233	0.071	-0.0859	0.4247	-0.0118	0.5127	-4.1291	6.4205	88.9653
7	7.7004	0.5089	-0.5525	3.9964	-0.2101	1.9818	-0.3022	-0.7776	-0.3104	-0.2586	-0.1477	0.6763	0.3602	-0.5884	0.519	0.4179	0.1025	0.0607	0.4888	-0.0146	0.3862	-2.1727	7.5706	97.4629
8	2.0491	-0.2581	-0.6946	2.187	1.0798	4.085	-0.1266	-0.3669	0.127	0.1595	0.2413	-0.0464	-0.5225	0.0718	-0.1418	0.3911	0.0365	-0.0022	0.2102	-0.0216	0.2738	7.1259	5.9065	90.3158
9	3.9833	1.3362	1.8907	5.7777	0.8356	0.8997	0.102	-0.5162	-0.4606	0.972	-0.2664	1.0846	-0.217	-1.7742	0.2368	0.593	0.0933	0.2166	1.1054	0.0113	0.4787	1.0565	1.8802	107.8406
10	3.4406	-1.2369	-0.3398	4.0344	1.9986	5.6326	-0.0009	-0.9023	-0.4281	0.5969	-0.0099	-0.3326	0.7222	0.8156	0.0546	0.4322	-0.0108	-0.0002	0.4899	0.1012	0.2503	14.2042	-5.4807	102.3593
11	2.7632	-0.3613	-1.011	3.2062	1.4368	3.4292	0.0306	-0.7152	0.1771	0.117	-0.0723	-0.3612	-0.5003	0.3786	0.0408	0.4875	-0.0573	-0.0192	0.543	-0.033	0.2655	17.434	7.5902	98.5497
12	1.1991	0.1546	0.988	1.3964	0.7306	1.9507	0.4594	-0.6725	-0.4684	0.6475	-0.2396	0.0275	0.5749	0.0531	-0.1144	0.608	-0.2196	-0.0237	0.5622	0.1388	0.4744	-2.692	-18.2333	89.1822
13	0.5032	0.0377	-0.4101	0.0084	-0.0393	0.3454	0.1789	-0.5359	-0.1228	0.3179	-0.0167	0.0674	-0.0513	0.1677	0.7365	1.085	-0.8627	0.4094	1.6207	0.0512	0.6331	-7.4032	-15.8578	104.1495
14	2.5258	0.3911	0.4086	1.7816	-0.1614	3.2821	0.2092	0.1919	-0.4406	-0.0623	-0.1696	0.0943	0.3483	-0.1259	0.0004	0.2854	-0.0203	0.0036	0.1404	-0.0215	0.2742	9.5366	-10.9495	82.6654
15	8.1888	0.1467	2.4681	0.0558	0.0983	1.4842	-0.0347	0.4537	-0.0433	0.0391	0.0447	-0.0552	-0.1707	0.4243	0.0324	0.2911	-0.0753	0.0112	0.348	0.0159	0.2441	17.1093	1.5854	74.0246
16	6.7263	-0.0215	-0.4623	2.8306	-4.6972	7.8774	0.0779	0.7842	-0.9798	-0.6735	0.4686	0.5716	1.854	-0.19	-0.4478	0.7316	-0.0199	-0.024	0.4448	-0.067	0.5479	16.1777	-18.4957	77.1144
17	5.8924	1.3852	-1.4646	1.8476	-0.9927	2.3363	-0.2011	0.1006	-0.6549	-0.2622	0.0727	-0.2846	0.5633	0.1928	0.1165	0.3913	0.0611	0.0365	0.2403	-0.0247	0.3323	20.6474	-11.9513	81.0321
18	3.7813	-1.181	5.3282	2.2043	-1.2142	7.575	-0.2161	2.1554	-1.0456	-1.1606	-0.1053	0.0299	0.0127	0.7833	0.3494	0.5947	0.0371	0.05	0.8477	-0.051	0.5098	27.8838	-4.9074	69.2539
19	6.0625	-0.6826	-0.119	3.5513	0.6713	1.9209	-0.084	0.0919	0.6679	0.295	-0.0004	-0.0544	-0.656	0.2602	0.0633	0.4032	-0.084	-0.0435	0.2655	0.0842	0.3017	22.3452	6.2926	79.4482
20	6.3754	-2.3379	0.0391	3.363	0.1098	2.7918	-0.1156	-0.6301	0.2262	0.1249	0.0118	-0.3746	0.0622	0.7363	0.0874	0.2766	-0.0104	0.0112	0.4692	0.0626	0.2601	28.3426	-2.2349	88.7173
21	4.1306	1.2006	-2.7185	2.025	-1.7467	3.9158	0.1244	0.4031	0.0643	-0.0053	-0.0609	0.2512	-0.0423	-0.4705	-0.0793	0.309	-0.031	0.002	0.6061	-0.0888	0.3349	3.8748	-2.7589	8.6915
22	2.0945	-0.0366	-0.1339	1.7504	1.4313	3.8875	-0.0554	-0.1027	-0.0885	0.2485	-0.0321	0.0377	0.2461	-0.2868	0.1055	0.258	-0.0376	0.0266	0.3192	-0.0058	0.2816	4.809	-2.6151	35.4919
23	1.9214	-0.0715	-0.0173	0.9404	1.2187	4.5556	-0.0338	-0.1938	0.1516	0.0771	0.0025	0.1037	-0.2545	-0.5076	0.0327	0.2891	0.0132	0.0222	0.3133	-0.0087	0.3205	4.589	7.195	36.2603
24	2.0377	1.6089	-0.3732	4.8536	-3.371	2.7017	0.2661	0.5461	-0.2213	0.8434	0.1438	0.1294	-0.1063	-1.1601	-0.1533	0.487	-0.162	0.0873	0.7877	-0.0302	0.5031	-3.3971	-1.0045	49.948
25	3.0108	0.5558	-0.501	4.114	0.3595	4.6123	-0.0096	-0.5867	0.1205	0.1925	0.0369	-0.4228	-0.0476	0.3467	-0.0149	0.2159	0.0465	-0.0228	0.3495	-0.0501	0.2766	16.9137	3.4316	42.2964
26	2.9252	0.5774	-0.4646	4.9935	-0.5131	1.6016	0.5496	-0.806	-0.7183	1.6057	-0.1391	0.025	1.5709	-1.2495	-0.292	0.919	-0.0868	0.1237	0.6096	0.0906	0.4817	2.151	-18.21	42.2194
27	1.7104	-0.2075	0.6502	0.9508	-0.6892	0.9247	-0.0126	0.366	-0.9109	0.005	0.1344	0.0123	0.9212	-0.903	-0.2985	0.5791	-0.3011	0.048	0.651	-0.0679	0.5327	-2.8756	-17.8017	27.4755
28	2.1338	1.4739	-0.9297	1.8079	-0.3738	2.9485	0.3087	-0.6615	-0.0221	0.7285	-0.3063	0.0113	0.1317	-0.115	0.038	0.9579	-0.7812	0.3196	0.9069	0.1298	0.3282	-5.2084	-15.1612	48.4386
29	4.1748	0.1453	-1.2026	0.6114	-0.2556	3.0999	-0.2035	0.0349	-0.3766	-0.0217	0.1124	-0.0382	0.6474	0.0319	0.0446	0.3654	-0.0478	0.0523	0.2419	-0.0611	0.3458	10.835	-11.2705	26.1992
30	7.9267	0.0453	0.8179	0.5846	0.0798	1.245	-0.1085	0.7204	0.0043	-0.0946	0.1236	-0.1571	-0.0681	0.0943	-0.0212	0.2362	-0.021	0.0195	0.425	-0.0367	0.2836	18.18	0.8283	15.8618
31	4.7802	-0.2726	-0.6417	7.0119	0.7875	3.5758	-0.2827	0.5195	-0.9364	-0.4806	0.2039	-0.5011	0.7186	-0.1905	0.1469	0.5336	-0.0112	0.048	0.3397	-0.1199	0.5773	21.8898	-15.934	19.2739
32	4.9515	-0.2652	-1.1691	1.2477	0.043	2.3552	-0.1796	-0.3345	-0.701	-0.1892	0.0923	-0.389	0.4609	0.159	0.1102	0.2944	0.0169	0.0554	0.1381	-0.0189	0.4024	20.6476	-10.3941	27.3938
33	0.4606	0.8195	-0.1335	3.187	-1.7882	1.4166	0.0298	1.3901	-0.6041	-1.1054	-0.445	-0.1431	-0.4265	0.3572	-0.6665	0.477	0.0838	0.0171	0.9037	-0.3549	0.4755	30.1698	-4.8533	12.2412
34	6.2917	-0.3328	-0.8859	4.0703	0.3846	1.9646	0.1538	0.3293	0.6504	-0.0417	-0.0434	-0.1267	-0.4881	-0.0285	-0.1302	0.2644	-0.0219	0.0032	0.2044	0.0481	0.2914	22.72	6.1051	20.6869
35	6.0763	-1.0831	0.766	3.7394	0.2437	2.818	-0.0667	-0.755	0.2156	0.152	0.1422	-0.4226	0.0896	0.5604	-0.0957	0.2185	0.0302	0.0018	0.4044	-0.0195	0.2632	29.6383	-1.4494	30.8773
36	4.9348	-0.8473	-0.6091	2.6092	-0.3937	1.9278	0.0178	0.0203	0.1787	-0.111	0.0999	-0.1791	0.1123	0.3173	-0.0996	0.3601	0.0067	-0.0044	0.5337	-0.0843	0.33	59.2269	-3.1798	22.3082
37	1.893	-0.5123	-1.2801	1.7976	0.2972	2.3977	0.0595	-0.1888	-0.011	-0.145	-0.0225	0.4029	-0.3251	-0.5722	-0.023	0.2233	0.0017	-0.0571	0.2973	-0.0063	0.3401	49.5425	3.3535	14.1016
38	3.3055	-3.1106	-0.8028	4.3831	0.2716	0.4056	0.1953	0.6842	-0.0947	-1.0382	-0.4392	0.3636	-0.624	-0.5414	0.1338	0.7126	0.0296	-0.1119	0.4239	0.0638	0.3149	54.096	7.3889	-11.6486
39	4.5509	0.3511	-3.255	7.2002	0.2613	7.5945	0.0886	-0.6335	0.4633	0.4806	-0.2351	1.3754	0.2192	-0.745	-0.0038	0.4182	-0.0566	-0.1659	0.5921	0.01	0.4865	42.5836	-5.1628	-1.2389
40	3.9756	0.3377	-1.2869	1.5535	-0.8008	3.3274	-0.0798	0.9439	0.0276	-0.421	-0.0018	0.3069	0.7705	-1.2872	-0.1439	0.4252	-0.0069	-0.2426	0.8176	-0.1281	0.6367	44.5071	-6.7988	-9.4095
41	1.5805	-0.458	-0.462	2.052	0.8192	1.8129	-0.1957	0.298	-0.2517	-0.3165	0.0859	0.3868	0.4634	-0.467	0.1909	0.4832	-0.1162	-0.104	0.2176	-0.0476	0.3334	53.6375	-5.8536	-2.3488
42	1.8269	-0.1378	-0.7444	1.9895	-0.7437	0.6173	-0.2911	1.7234	0.8852	-1.4723	-0.0569	0.6982	-0.0435	-0.9896	0.3338	0.8722	-0.1396	-0.3464	1.3756	0.1537	0.7348	47.7988	-1.9275	-20.2808
43	2.7392	-0.3955	0.6712	2.505	-0.1166	3.9836	0.0369	0.5809	-0.0379	-0.714	-0.0304	-0.4181	-0.0966	0.3922	-0.0034	0.5535	-0.0352	-0.0302	0.2848	0.0083	0.2688	63.1395	-2.1204	-12.0584
44	2.0505	0.3277	-1.4477	0.6888	1.2844	4.6794	0.3339	1.0062	0.6095	-0.9638	-0.3068	0.323	-0.5644	0.0212	0.2172	0.9491	0.1999	-0.1605	0.5543	0.2146	0.5383	45.2031	21.9267	-6.7247
45	2.7072	-0.3963	-0.1067	1.5914	-0.1818	2.686	0.3658	0.3447	0.3295	-0.7462	-0.1099	0.4167	-0.7846	-0.4115	0.0004	0.6528	0.1841	-0.2629	0.3766	0.0224	0.4246	48.6402	14.9606	0.105
46	6.5417	0.1636	-0.7294	1.4509	-0.0147	2.725	-0.1133	0.2682	0.0239	-0.0538	0.2076	-0.0178	0.1009	0.4002	-0.0947	0.208	0.0094	-0.0387	0.2186	-0.0195	0.1971	63.6789	-1.5659	14.5222
47	5.8071	-0.6027	0.6028	5.2816	-1.6007	3.4918	-0.4282	-0.6199	0.9184	0.4788	0.2501	0.2718	-1.1695	-0.0597	0.2445	0.6349	-0.1046	-0.0328	0.4416	-0.1736	0.4868	68.5487	15.386	11.8565
48	4.2659	-0.2874	-0.1862	1.5606	0.0338	1.7508	-0.4526	-0.093	0.4765	-0.0593	0.2738	-0.2734	-0.7817	0.4213	0.1619	0.3586	-0.1169	-0.06	0.3495	-0.0509	0.3105	69.1471	8.6957	7.3512
49	3.4935	0.5714	0.6897	2.7982	0.5105	2.2288	-0.0779	0.082	-0.2323	-0.2376	0.2433	-0.2178	0.1599	0.926	-0.0929	0.2595	0.0065	0.0088	0.4241	-0.0478	0.2629	72.3027	-2.6829	4.4036
50	2.9968	-1.951	0.1947	4.4581	0.9556	4.1043	0.1379	-0.5825	0.0295	0.5006	0.0465	-0.3957	1.2175	0.0156	0.028	0.5355	0.0324	-0.0049	0.2739	0.0306	0.2806	51.3227	-2.4796	81.1587
51	3.9092	-1.6087	0.9875	2.7617	-0.7315	5.0407	-0.0738	-0.4074	-0.1209	0.3693	0.2028	0.0381	-0.0873	0.017	-0.1283	0.2909	0.0108	0.052	0.2837	0.0055	0.2713	48.5735	4.4576	79.1403
52	0.8965	0.134	-0.3378	0.8434	0.7226	2.5467	-0.0026	0.0721	-0.0449	-0.0634	-0.0234	0.0508	-0.0277	-0.2359	0.0453	0.1785	0.0221	-0.0002	0.1373	0.0188	0.1909	51.9334	-0.4352	53.2493
53	2.881	-1.4712	0.469	5.4111	4.2767	5.88	-0.0344	0.1915	0.1892	-0.4285	-0.095	-0.0318	-0.7662	-0.1168	0.1474	0.3786	0.0955	0.0386	0.2739	0.0634	0.2481	50.541	13.7033	49.9009
54	2.9959	0.8585	-0.4163	5.8444	-1.7643	8.0079	-0.0109	-0.2942	-0.3143	0.0708	0.039	0.5521	0.2728	-0.9145	-0.0196	0.1841	-0.0198	0.0169	0.2961	0.0084	0.3309	43.9257	-7.3012	52.0312
55	0.2643	-0.0406	-0.6225	1.0135	1.6904	3.0312	-0.0636	-0.043	-0.1039	0.0201	0.0326	0.0135	0.242	-0.2147	-0.0123	0.2564	-0.0301	0.0148	0.1422	0.0132	0.2549	53.3944	-6.2633	55.7124
56	3.4984	-3.1846	0.6482	7.7153	0.8916	2.4339	-0.0189	-0.149	-0.1937	0.1345	-0.0594	0.8343	-0.2421	-0.5501	0.1371	0.3416	-0.0509	0.0207	0.4268	-0.0225	0.4364	43.5322	-0.6633	40.6151
57	2.238	-0.4975	-0.2867	2.6008	0.4314	4.5418	0.0395	0.1277	0.0221	0.0259	0.0575	-0.312	-0.0408	0.1979	-0.0827	0.1415	-0.0229	0.0144	0.1273	0.011	0.209	62.377	-2.6048	45.6693
58	1.2316	-1.2558	-0.9853	2.3931	3.1807	4.835	0.4573	0.4524	0.4253	-0.9103	-0.0754	0.106	-1.754	-0.1655	-0.2609	0.6598	0.0766	-0.0105	0.2934	0.0402	0.3462	44.8201	18.634	47.7828
59	1.2122	0.192	0.5594	0.3315	-0.3519	6.8109	0.1081	0.1193	0.2743	-0.1933	-0.2507	0.2546	-0.3496	-0.4394	0.1952	0.4277	0.1469	-0.0089	0.2233	-0.0034	0.3228	41.658	16.7707	61.7477
60	0.9496	-0.2498	-0.2619	1.2928	-0.2011	2.1495	0.2811	0.3048	-0.0418	-0.2186	-0.1011	0.1063	-0.315	-0.1965	-0.1724	0.3065	0.1148	-0.0195	0.2311	-0.0567	0.2277	50.4069	11.8418	55.8009
61	6.5029	1.2477	-1.5465	0.7861	-0.1261	1.859	-0.0197	0.0219	-0.2304	0.2023	0.1296	-0.1787	0.2145	0.3849	-0.099	0.2701	0.0649	-0.0265	0.2495	0.02	0.2352	64.2974	-0.6761	72.0693
62	5.4326	-0.3801	1.1154	1.6426	-0.2094	1.1271	-0.2007	-0.3446	0.6218	0.2368	0.171	-0.2948	-0.3346	0.0696	0.0184	0.3363	-0.0131	-0.0254	0.2435	-0.0818	0.3186	66.0297	13.5069	64.4718
63	4.7475	-1.3172	-4.9703	3.3019	-0.9801	7.0283	-0.6166	-2.0517	0.6741	0.7306	-0.1055	0.2753	-0.2088	1.368	0.0048	0.5465	0.0724	-0.0756	0.9136	-0.308	0.506	74.909	5.8605	75.9859
64	4.3074	0.6239	-0.2183	3.5301	-0.1642	0.9404	-0.0511	-0.6206	-0.5684	0.1841	0.0334	-0.1741	0.3913	0.2371	-0.013	0.2632	0.074	-0.0165	0.2595	0.0649	0.2506	69.118	-5.6349	66.6944
65	6.3024	1.3938	-0.7775	2.189	0.166	2.111	-0.1649	0.4906	-0.3636	-0.1184	0.0885	-0.3639	-0.047	0.5017	0.0515	0.2018	-0.0039	-0.0109	0.3937	0.0192	0.2793	74.6188	2.6664	56.915

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 48 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 49 through 66 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 67 through 94 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 95 through 104 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 105 through 117 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 118 through 147 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 148 through 166 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 167 through 187 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 188 through 209 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 6 through 38 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 39 through 48 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 49 through 66 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 67 through 94 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 95 through 104 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 105 through 147 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 148 through 166 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 167 through 187 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 188 through 209 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 7 through 48 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 49 through 104 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 105 through 152 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 153 through 166 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 167 through 210 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 6 through 23 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 24 through 38 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 39 through 48 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 49 through 66 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 67 through 93 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 94 through 117 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 118 through 147 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 148 through 166 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 167 through 187 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 188 through 210 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid -4 through 23 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 24 through 66 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 67 through 94 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 95 through 104 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 105 through 117 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 118 through 147 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 148 through 166 )
43	X-RAY DIFFRACTION	43	chain 'E' and (resid 167 through 209 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 11 through 23 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 24 through 66 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 67 through 93 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 94 through 117 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 118 through 166 )
49	X-RAY DIFFRACTION	49	chain 'F' and (resid 167 through 209 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 8 through 23 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 24 through 48 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 49 through 78 )
53	X-RAY DIFFRACTION	53	chain 'G' and (resid 79 through 93 )
54	X-RAY DIFFRACTION	54	chain 'G' and (resid 94 through 117 )
55	X-RAY DIFFRACTION	55	chain 'G' and (resid 118 through 147 )
56	X-RAY DIFFRACTION	56	chain 'G' and (resid 148 through 166 )
57	X-RAY DIFFRACTION	57	chain 'G' and (resid 167 through 210 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 7 through 23 )
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 24 through 38 )
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 39 through 66 )
61	X-RAY DIFFRACTION	61	chain 'H' and (resid 67 through 93 )
62	X-RAY DIFFRACTION	62	chain 'H' and (resid 94 through 147 )
63	X-RAY DIFFRACTION	63	chain 'H' and (resid 148 through 166 )
64	X-RAY DIFFRACTION	64	chain 'H' and (resid 167 through 187 )
65	X-RAY DIFFRACTION	65	chain 'H' and (resid 188 through 209 )

-
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