PDB-3tqu: Structure of a HAM1 protein from Coxiella burnetii

ID or keywords:

Entry

Database: PDB / ID: 3tqu

Title

Structure of a HAM1 protein from Coxiella burnetii

Components

Non-canonical purine NTP pyrophosphatase

Keywords

HYDROLASE / HAM1 protein

Function / homology

Function and homology information

XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity /

nucleotide binding /

metal ion binding ...
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Cheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 27, 2016	Group: Database references
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3tqu.cif.gz	343.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3tqu.ent.gz	280.2 KB	Display	PDB format
PDBx/mmJSON format	3tqu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqu ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqu	HTTPS FTP

-
Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C 1k7kS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zve-2 5zvd-2 5zvd-1 5zvh-1 5zvg-2 6pwj-2 5zvg-1 2c5u-2 5zvh-2 3ezx-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Non-canonical purine NTP pyrophosphatase

B: Non-canonical purine NTP pyrophosphatase

C: Non-canonical purine NTP pyrophosphatase

D: Non-canonical purine NTP pyrophosphatase

hetero molecules

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

1

A: Non-canonical purine NTP pyrophosphatase

B: Non-canonical purine NTP pyrophosphatase

hetero molecules

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

2

C: Non-canonical purine NTP pyrophosphatase

D: Non-canonical purine NTP pyrophosphatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.528, 86.737, 105.794
Angle α, β, γ (deg.)	90.000, 92.490, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Non-canonical purine NTP pyrophosphatase / Non-standard purine NTP pyrophosphatase / Nucleoside-triphosphate diphosphatase / Nucleoside- ...Non-standard purine NTP pyrophosphatase / Nucleoside-triphosphate diphosphatase / Nucleoside-triphosphate pyrophosphatase / NTPase Mass: 22212.311 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0043 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q83FA3, nucleoside-triphosphate diphosphatase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1245 / 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: 2.66 Å³/Da / Density % sol: 53.73 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M calcium chloride, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 26, 2011

Radiation

Monochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.9→30 Å / Num. all: 73391 / Num. obs: 72951 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / R_merge(I) obs: 0.083 / Χ²: 1.042 / Net I/σ(I): 7.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.9-1.93	2	0.484	3475	0.98	1	95.3
1.93-1.97	2.2	0.385	3518	0.941	1	97.1
1.97-2.01	2.3	0.318	3592	0.968	1	98.5
2.01-2.05	2.5	0.268	3618	0.943	1	99.4
2.05-2.09	2.7	0.239	3646	1.002	1	99.7
2.09-2.14	2.8	0.212	3687	0.925	1	99.8
2.14-2.19	3	0.193	3644	0.935	1	99.9
2.19-2.25	3.4	0.186	3669	0.954	1	100
2.25-2.32	3.5	0.17	3639	0.91	1	100
2.32-2.39	3.5	0.157	3648	0.946	1	99.9
2.39-2.48	3.5	0.148	3677	0.916	1	99.9
2.48-2.58	3.6	0.134	3680	0.981	1	100
2.58-2.7	3.6	0.112	3642	0.962	1	100
2.7-2.84	3.6	0.095	3672	0.914	1	100
2.84-3.02	3.6	0.089	3686	1.007	1	100
3.02-3.25	3.7	0.07	3658	1.043	1	100
3.25-3.57	3.6	0.055	3657	1.123	1	99.9
3.57-4.09	3.7	0.052	3706	1.443	1	100
4.09-5.15	3.7	0.051	3715	1.352	1	99.9
5.15-30	3.4	0.046	3722	1.314	1	98.7

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1K7K

1k7k

Resolution: 1.9→22.755 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.8499 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2447	3680	5.05 %	RANDOM
R_work	0.1995	-	-	-
all	0.2018	77061	-	-
obs	0.2018	72911	99.39 %	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.467 Å² / k_sol: 0.364 e/Å³

Displacement parameters

B_iso max: 74.61 Å² / B_iso mean: 22.6624 Å² / B_iso min: 1.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.4934 Å²	0 Å²	0.7864 Å²
2-	-	-0.0181 Å²	0 Å²
3-	-	-	2.5115 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→22.755 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6020	0	9	1245	7274

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6163
X-RAY DIFFRACTION	f_angle_d	0.7	8358
X-RAY DIFFRACTION	f_chiral_restr	0.05	944
X-RAY DIFFRACTION	f_plane_restr	0.003	1124
X-RAY DIFFRACTION	f_dihedral_angle_d	13.152	2297

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.9239	0.3904	104	0.3552	2537	2641	94
1.9239-1.9503	0.3649	139	0.3055	2560	2699	97
1.9503-1.9781	0.3004	142	0.2497	2638	2780	98
1.9781-2.0076	0.2662	148	0.2288	2581	2729	99
2.0076-2.039	0.2656	136	0.2086	2665	2801	100
2.039-2.0724	0.2534	134	0.206	2689	2823	100
2.0724-2.1081	0.2407	151	0.201	2637	2788	100
2.1081-2.1464	0.2417	133	0.192	2670	2803	100
2.1464-2.1877	0.2575	149	0.1953	2645	2794	100
2.1877-2.2323	0.2951	148	0.2003	2677	2825	100
2.2323-2.2808	0.2472	119	0.1988	2691	2810	100
2.2808-2.3338	0.2462	137	0.1985	2676	2813	100
2.3338-2.3921	0.2608	148	0.1888	2643	2791	100
2.3921-2.4567	0.2429	150	0.1895	2716	2866	100
2.4567-2.5289	0.2437	152	0.1956	2618	2770	100
2.5289-2.6104	0.2396	138	0.1959	2663	2801	100
2.6104-2.7035	0.2324	131	0.1972	2718	2849	100
2.7035-2.8116	0.2392	164	0.1986	2645	2809	100
2.8116-2.9393	0.2559	139	0.2059	2676	2815	100
2.9393-3.0939	0.2669	146	0.203	2679	2825	100
3.0939-3.2872	0.2511	137	0.1896	2709	2846	100
3.2872-3.5402	0.2279	152	0.1938	2664	2816	100
3.5402-3.8948	0.2183	144	0.1772	2696	2840	100
3.8948-4.4547	0.1969	135	0.162	2697	2832	100
4.4547-5.5987	0.2217	152	0.1816	2716	2868	100
5.5987-22.7563	0.246	152	0.2393	2725	2877	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	1.0122	-0.2915	0.7934	0.1899	0.3316	3.6249	0.0638	-0.1983	0.0176	0.0062	0.091	0.1322	-0.382	-0.2575	-0.1065	0.1219	-0.0163	0.0159	0.1382	-0.0159	0.1675	22.8389	50.6913	113.7025
2	1.0554	-0.202	-0.1384	1.6936	0.1163	1.9135	0.0972	0.0103	-0.2843	-0.235	-0.1491	0.0522	0.1609	0.5912	0.0018	0.1149	0.0271	0.035	0.1325	0.0101	0.1541	19.3498	41.9547	111.015
3	0.34	-0.3225	0.1312	2.0101	-1.034	0.7112	0.0923	-0.0276	-0.0114	-0.451	0.1406	0.1436	0.2077	0.0491	-0.0405	0.0789	0.0244	0.0113	0.087	-0.0258	0.1772	21.3185	48.5721	116.8412
4	0.4406	-0.4975	0.0515	0.9432	0.2287	0.1162	0.2575	0.0914	-0.0445	-0.3219	-0.2781	0.1492	-0.2804	-0.001	-0.0338	0.1459	0.0093	0.008	0.0924	-0.0103	0.0862	28.4399	55.7384	99.0183
5	0.1159	0.1826	-0.109	0.2419	0.0813	-0.0127	0.0155	0.0446	0.0774	-0.065	-0.0508	0.0145	-0.0453	-0.1184	-0.0083	0.0707	-0.0081	0.0001	0.0999	0.0003	0.1067	31.1186	49.7795	102.4284
6	1.6929	-0.2856	-0.0492	0.2549	0.0244	0.362	-0.0162	0.2626	0.7816	-0.1723	0.0075	-0.0688	-0.1413	-0.0418	0.2304	0.2092	-0.0153	-0.0365	0.125	0.0693	0.2247	26.1574	45.7574	87.3895
7	0.975	-0.3578	0.2101	0.7844	0.1098	0.1945	-0.015	0.6655	0.4071	-0.7137	0.0879	0.1318	-0.2175	-0.2424	-0.0711	0.2815	-0.093	0.0087	0.2685	0.0696	0.1052	22.6952	37.8571	81.7239
8	0.6093	0.1237	0.2378	0.1653	0.0226	0.3279	-0.0149	-0.0079	-0.1025	-0.2643	-0.075	-0.0879	-0.2465	-0.1763	0.0396	0.1251	-0.0154	0.0144	0.0534	0.0056	0.0864	32.2334	38.3634	96.3494
9	0.6002	0.1901	0.0559	0.1008	0.192	0.2991	0.038	-0.0319	-0.0023	0.1129	-0.0571	-0.0282	0.1606	0.0289	0.0204	0.0892	0.0073	-0.0043	0.0636	0.0118	0.0837	34.8419	43.5679	106.3054
10	0.2763	0.2304	-0.2578	0.4767	-0.2352	0.2026	-0.0418	0.0119	-0.0977	-0.0912	0.1043	0.0155	0.0762	-0.1191	0.0008	0.1092	-0.0119	0.0085	0.0696	-0.0236	0.109	19.7653	29.0976	95.3063
11	0.6281	-0.2222	-0.1316	0.6916	-0.0783	0.425	-0.1977	-0.0782	-0.1674	0.1052	0.2091	0.1224	0.0929	0.0195	-0.0099	0.1271	0.0186	0.0104	0.1064	0.0268	0.1012	30.2489	37.4765	112.6254
12	0.7916	-0.0898	-0.1223	0.8439	0.3013	0.8167	-0.167	-0.0095	-0.4217	-0.3663	-0.0805	-0.3289	-0.0719	0.2585	0.0922	0.1823	0.0249	0.0315	0.1299	0.017	0.2037	56.4936	39.1499	94.6303
13	0.9041	-0.396	-0.2488	1.544	0.1354	0.9479	0.0836	-0.2697	-0.4673	0.1201	-0.3366	0.3308	0.0152	0.0187	0.1434	0.1438	0.0047	0.0495	0.2192	0.0086	0.2455	60.0453	37.4875	103.5574
14	0.7281	0.1549	0.2016	1.2211	0.0487	0.568	0.2208	0.233	-0.2256	0.5949	-0.4054	-0.4335	0.155	0.4017	0.0716	0.2112	0.0416	0.0452	0.1042	0.019	0.2234	57.9933	35.425	95.0775
15	0.5163	0.2005	-0.1743	0.4782	-0.5725	0.7124	-0.2068	-0.2537	0.0695	-0.0606	-0.1329	-0.4355	-0.5068	0.1623	-0.1732	0.2048	-0.0793	0.1295	-0.0044	0.086	0.1975	50.6394	54.6454	96.8302
16	-0.1633	-0.1909	0.0703	-0.0398	0.1819	0.2862	0.0318	0.0268	0.0443	-0.0257	-0.0591	-0.0656	-0.1461	-0.0094	0.0082	0.0592	0.0012	0.0019	0.0928	-0.0018	0.0697	48.2897	48.8519	100.7191
17	2.3303	0.4091	-1.1163	0.3569	-0.4252	0.765	0.3605	0.1537	0.161	0.0516	-0.1566	0.1831	-0.3386	-0.0022	-0.0825	0.1816	-0.0079	-0.0117	0.159	-0.0221	0.1842	52.9508	59.6544	110.7593
18	1.6961	-0.5036	-0.7335	0.3075	0.2283	0.9403	-0.305	0.3724	0.5553	-0.0103	0.0494	-0.2637	-0.3701	-0.068	-0.0384	0.109	-0.0018	-0.036	0.0337	-0.0854	0.1249	56.6864	61.7535	120.2958
19	0.4875	-0.1681	-0.1866	0.3848	0.2219	0.2531	-0.205	-0.1522	0.0393	-0.1821	0.009	0.2191	-0.3428	0.0291	-0.0746	0.1112	0.0309	-0.0302	0.106	-0.0348	0.0665	47.1657	48.9739	113.6205
20	0.2867	0.247	0.2218	-0.1329	0.016	0.6453	0.0392	0.0558	-0.0636	0.006	0.1258	0.0445	0.1136	0.1492	-0.0362	0.1377	0.0183	0.0077	0.0825	-0.003	0.0945	44.5286	42.5706	104.4269
21	0.3501	-0.1819	0.1176	0.9397	0.0491	0.2493	0.0763	-0.1999	0.213	-0.0819	0.0371	-0.2242	0.0861	0.0098	-0.0692	0.0558	-0.011	-0.0121	0.1009	-0.0383	0.0368	60.9163	51.5401	121.8721
22	0.1564	-0.1398	0.0529	0.2421	-0.0035	0.2665	-0.0902	-0.0796	-0.1645	0.2463	0.0676	0.0157	0.1227	0.1981	0.0206	0.1511	0.0171	0.0132	0.1288	0.0206	0.0964	58.7419	41.5167	122.5519
23	0.386	-0.0152	-0.1639	0.0405	-0.1052	0.7001	0.0171	-0.2627	-0.305	-0.1536	-0.1182	0.0355	0.2872	-0.2914	-0.0004	0.178	0.0051	-0.0108	0.0629	0.0419	0.2229	49.3016	34.0302	107.0505
24	0.5393	0.1955	0.4074	0.1801	0.0114	0.375	-0.0231	-0.1	0.1474	0.0518	-0.1589	-0.0388	-0.0585	0.0552	-0.0023	0.094	-0.0144	-0.0279	0.1346	-0.0141	0.1616	55.7058	55.1627	166.6727
25	0.4926	-0.0998	0.482	0.0446	-0.2078	0.7887	0.3104	0.2049	-0.2828	0.3898	-0.206	-0.0539	0.4487	0.5014	-0.1253	0.269	-0.0053	-0.0744	0.1733	0.0335	0.1696	48.1026	37.5635	166.9711
26	0.1062	-0.1157	0.2702	0.029	0.0317	0.2884	0.0096	-0.0139	-0.0452	0.0254	-0.0689	0.0039	0.1229	-0.0178	0.0197	0.0664	-0.0154	0.0132	0.1098	0.0149	0.0843	45.7529	43.4024	163.2661
27	0.5184	-0.3743	-0.2077	0.7228	-0.0524	0.1408	0.077	-0.2595	-0.5078	-0.005	-0.0042	0.2134	0.0676	-0.0316	-0.0544	0.1649	-0.02	0.0172	0.1354	0.0474	0.1824	50.4187	32.5939	152.9373
28	0.557	0.4266	0.4988	0.5553	0.2129	0.4406	-0.2054	-0.0964	-0.3733	-0.1006	0.083	-0.1808	0.1102	-0.1521	-0.0377	0.1188	-0.0372	0.0361	0.1269	-0.0525	0.1379	54.1177	30.9028	143.1693
29	1.013	-0.2694	-0.3169	0.0946	-0.1724	0.1457	0.0398	-0.0613	0.0479	-0.0369	0.0294	0.0233	-0.1222	0.0997	-0.0291	0.0877	-0.0244	0.0172	0.0939	0.0007	0.0819	43.234	46.5766	154.984
30	0.4816	0.219	-0.1524	0.2503	-0.0644	0.0359	-0.2159	0.1417	-0.045	-0.1135	0.1341	-0.1637	-0.1638	-0.1882	0.0351	0.1571	0.0113	0.006	0.1178	-0.0014	0.0665	56.6071	43.3293	140.6173
31	0.5381	0.0907	0.1076	0.3222	-0.4121	0.6437	0.0098	0.0796	0.3042	0.0091	0.1007	0.0807	-0.075	0.1296	-0.0342	0.125	-0.0051	0.0302	0.1156	-0.0049	0.1038	57.8061	52.0238	142.9329
32	0.2668	-0.176	0.3259	0.1677	-0.1706	0.6421	-0.0364	0.1019	0.3374	-0.0337	-0.0054	0.1108	-0.1854	-0.0625	0.0134	0.1312	0.0062	0.0322	0.0813	0.0047	0.1896	46.791	58.3193	157.3405
33	0.1407	0.0064	0.1817	0.0666	0.0648	0.2724	-0.1381	0.0568	-0.1624	-0.0596	-0.1299	0.0991	0.1846	0.1065	0.059	0.1521	-0.0099	0.0178	0.1471	-0.0264	0.0807	20.3473	41.8041	150.0848
34	0.9361	0.7952	-0.5778	0.6682	-0.2776	1.7222	0.038	-0.0464	0.335	0.1244	0.025	0.0313	-0.1818	0.3365	-0.0057	0.1209	-0.0267	-0.0224	0.1383	0.0085	0.136	16.7831	50.4411	152.9553
35	0.083	-0.0046	0.0241	0.4608	-0.1268	0.2574	0.1592	0.0796	-0.0967	0.122	0.0764	0.2769	-0.064	0.1509	-0.0283	0.102	-0.0459	-0.0276	0.1038	-0.0041	0.1465	18.8242	43.9004	146.9596
36	1.2837	0.9858	0.2752	1.5346	0.5178	0.1212	0.474	-0.1779	0.032	0.5907	-0.3418	0.1102	0.4352	-0.1533	-0.0709	0.1669	-0.0436	0.0034	0.1392	0.0302	0.1043	25.944	36.4085	164.7143
37	0.3353	-0.0195	0.1837	0.1611	0.1937	-0.0402	0.0269	0.0247	-0.0901	0.0091	0.003	0.0156	0.0039	-0.0531	-0.0074	0.0668	-0.0049	0.001	0.0857	0.0121	0.0969	28.5975	42.4159	161.4872
38	1.1864	0.4856	-0.2615	0.6697	0.081	0.7122	-0.0601	-0.0754	-0.4525	0.6082	0.003	-0.1343	0.4692	0.2513	0.1321	0.2023	0.0064	0.0979	0.0908	0.0737	0.168	23.5673	46.1993	176.3791
39	1.2362	0.0114	0.3427	0.243	0.2384	0.3964	-0.1574	-0.02	-0.4203	0.5333	0.2479	0.0602	0.103	0.1578	-0.0169	0.2156	-0.0016	-0.0174	0.1386	0.0322	0.0659	20.0208	53.9411	182.3506
40	1.3351	-0.0818	-0.3442	0.7656	0.3855	0.5544	-0.0217	-0.0721	-0.015	0.0998	-0.0049	-0.1362	-0.0497	0.0695	0.0013	0.1117	0.009	-0.0087	0.0909	0.0037	0.0704	31.1612	51.2158	162.8262
41	0.6132	-0.3283	0.1314	0.2584	-0.1662	0.1793	-0.0618	-0.1306	-0.266	0.183	0.2057	0.2284	-0.1912	-0.111	-0.0152	0.1353	0.0127	0.0212	0.0757	-0.0063	0.1206	16.0689	60.1647	174.2136
42	0.5107	-0.1634	-0.0282	0.457	-0.2368	0.3326	-0.0794	0.0439	0.1078	0.087	0.0031	0.0262	-0.1373	-0.0253	0.0541	0.1121	-0.0036	-0.0193	0.0803	-0.0137	0.1077	18.3926	65.2198	165.4809
43	0.6359	0.1224	0.1117	0.3184	-0.1525	0.0972	-0.171	0.1802	0.1204	-0.1701	0.0943	-0.015	-0.0754	-0.0234	0.0167	0.159	-0.0118	0.0248	0.113	0.0105	0.0906	27.708	55.0143	151.518

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:10)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 11:20)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 21:34)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 35:45)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 46:77)	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 78:94)	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 95:109)	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 110:125)	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 126:143)	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 144:181)	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 182:197)	A
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 1:10)	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 11:20)	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 21:34)	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 35:45)	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 46:77)	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 78:94)	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 95:109)	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 110:125)	B
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 126:143)	B
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 144:159)	B
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 160:181)	B
23	X-RAY DIFFRACTION	23	chain 'B' and (resseq 182:197)	B
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 1:34)	C
25	X-RAY DIFFRACTION	25	chain 'C' and (resseq 35:45)	C
26	X-RAY DIFFRACTION	26	chain 'C' and (resseq 46:77)	C
27	X-RAY DIFFRACTION	27	chain 'C' and (resseq 78:94)	C
28	X-RAY DIFFRACTION	28	chain 'C' and (resseq 95:109)	C
29	X-RAY DIFFRACTION	29	chain 'C' and (resseq 110:143)	C
30	X-RAY DIFFRACTION	30	chain 'C' and (resseq 144:165)	C
31	X-RAY DIFFRACTION	31	chain 'C' and (resseq 166:181)	C
32	X-RAY DIFFRACTION	32	chain 'C' and (resseq 182:197)	C
33	X-RAY DIFFRACTION	33	chain 'D' and (resseq 1:10)	D
34	X-RAY DIFFRACTION	34	chain 'D' and (resseq 11:20)	D
35	X-RAY DIFFRACTION	35	chain 'D' and (resseq 21:34)	D
36	X-RAY DIFFRACTION	36	chain 'D' and (resseq 35:45)	D
37	X-RAY DIFFRACTION	37	chain 'D' and (resseq 46:77)	D
38	X-RAY DIFFRACTION	38	chain 'D' and (resseq 78:94)	D
39	X-RAY DIFFRACTION	39	chain 'D' and (resseq 95:109)	D
40	X-RAY DIFFRACTION	40	chain 'D' and (resseq 110:143)	D
41	X-RAY DIFFRACTION	41	chain 'D' and (resseq 144:159)	D
42	X-RAY DIFFRACTION	42	chain 'D' and (resseq 160:181)	D
43	X-RAY DIFFRACTION	43	chain 'D' and (resseq 182:197)	D

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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