PDB-4e1v: X-RAY Structure of the Uridine Phosphorylase from Salmonella Typh...

ID or keywords:

Entry

Database: PDB / ID: 4e1v

Title

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution

Components

Uridine phosphorylase

Keywords

TRANSFERASE / Rossmann Fold / drug metabolism

Function / homology

Function and homology information

nucleotide catabolic process / deoxyuridine phosphorylase activity / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / cytosol
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.15 Å

Authors

Lashkov, A.A. / Sotnichenko, S.E. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Mikhailov, A.M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae.
Authors: Lashkov, A.A. / Sotnichenko, S.E. / Prokofiev, I.I. / Gabdulkhakov, A.G. / Agapov, I.I. / Shtil, A.A. / Betzel, C. / Mironov, A.S. / Mikhailov, A.M.

History

Deposition	Mar 7, 2012	Deposition site: RCSB / Processing site: RCSB
Supersession	Mar 6, 2013	ID: 3NSR
Revision 1.0	Mar 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	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_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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4e1v.cif.gz	830.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4e1v.ent.gz	701 KB	Display	PDB format
PDBx/mmJSON format	4e1v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e1/4e1v ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1v	HTTPS FTP

-
Related structure data

Related structure data	3fwpS S: Starting model for refinement
Similar structure data	2hwu-d 3ddo-d 4r2x-d 4r2w-d 1y1q-d 1y1r-d 1zl2-d 1rxs-4 3fwp-d 2oec-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Uridine phosphorylase

E: Uridine phosphorylase

F: Uridine phosphorylase

D: Uridine phosphorylase

C: Uridine phosphorylase

B: Uridine phosphorylase

H: Uridine phosphorylase

I: Uridine phosphorylase

G: Uridine phosphorylase

hetero molecules

246 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uridine phosphorylase

E: Uridine phosphorylase

F: Uridine phosphorylase

D: Uridine phosphorylase

C: Uridine phosphorylase

B: Uridine phosphorylase

hetero molecules

defined by author&software
164 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Uridine phosphorylase

I: Uridine phosphorylase

G: Uridine phosphorylase

hetero molecules

H: Uridine phosphorylase

I: Uridine phosphorylase

G: Uridine phosphorylase

hetero molecules

defined by author&software
164 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	158.490, 93.210, 149.970
Angle α, β, γ (deg.)	90.000, 90.820, 90.000
Int Tables number	5
Space group name H-M	C121

-
Protein , 1 types, 9 molecules AEFDCBHIG

#1: Protein	Uridine phosphorylase / UPase / UrdPase Mass: 27169.092 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: STM3968, STMD1.21, udp / Plasmid: PBLUESCRIPT IISK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P0A1F6, uridine phosphorylase

#1: Protein

Uridine phosphorylase / UPase / UrdPase

Mass: 27169.092 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM3968, STMD1.21, udp / Plasmid: PBLUESCRIPT IISK / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P0A1F6, uridine phosphorylase

-
Non-polymers , 5 types, 443 molecules

#2: Chemical	ChemComp-URF / 5-FLUOROURACIL Mass: 130.077 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₃FN₂O₂ / Comment: medication, chemotherapy*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.26 Å³/Da / Density % sol: 45.69 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 20% PEG 4000, 0.2M magnesium chloride, 0.1M cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.918 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 5, 2008

Radiation

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

Radiation wavelength

Wavelength: 0.918 Å / Relative weight: 1

Reflection

Resolution: 2.15→30 Å / Num. all: 118761 / Num. obs: 115000 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / R_merge(I) obs: 0.069 / Net I/σ(I): 12.11

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.15-2.2	0.64	1.89	23563	7687	1	97.3
2.2-2.3	0.52	2.3	43019	13604	1	98.6
2.3-2.5	0.365	3.27	66607	20991	1	98.5
2.5-2.7	0.232	5.19	48418	15218	1	98.1
2.7-3	0.121	9.39	50539	15826	1	97.5
3-3.5	0.065	19.49	74278	15641	1	96.7
3.5-4	0.037	25.4	27510	8706	1	95.5
4-5	0.032	29.52	27010	8544	1	94.5
5-6	0.034	28.41	12084	3749	1	93.4
6-8	0.027	31.52	9641	2991	1	92.7
8-10	0.024	35.85	3270	1031	1	88.7
10-30	0.023	33.92	3011	1012	1	80.8

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.1	data extraction
DENZO		data reduction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3FWP

3fwp

Resolution: 2.15→28.875 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8257 / SU ML: 0.29 / σ(F): 2.01 / Phase error: 25.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2383	5749	5 %	RANDOM
R_work	0.1938	-	-	-
all	0.196	115000	-	-
obs	0.196	114973	96.86 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.312 Å² / k_sol: 0.343 e/Å³

Displacement parameters

B_iso max: 137.72 Å² / B_iso mean: 54.9412 Å² / B_iso min: 8.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.5701 Å²	0 Å²	-3.4549 Å²
2-	-	9.5857 Å²	-0 Å²
3-	-	-	-6.0157 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→28.875 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16487	0	109	426	17022

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	16875
X-RAY DIFFRACTION	f_angle_d	0.966	22859
X-RAY DIFFRACTION	f_chiral_restr	0.065	2690
X-RAY DIFFRACTION	f_plane_restr	0.004	2946
X-RAY DIFFRACTION	f_dihedral_angle_d	14.386	6093

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.15-2.1744	0.3076	189	0.3093	3593	3782	96
2.1744-2.2	0.3357	195	0.29	3711	3906	99
2.2-2.2268	0.327	192	0.2829	3649	3841	98
2.2268-2.255	0.3295	195	0.2755	3713	3908	99
2.255-2.2847	0.3383	193	0.2624	3660	3853	98
2.2847-2.3159	0.3337	195	0.2682	3701	3896	99
2.3159-2.349	0.2893	195	0.2512	3705	3900	98
2.349-2.3841	0.2892	194	0.2504	3688	3882	99
2.3841-2.4213	0.2913	195	0.2457	3702	3897	98
2.4213-2.461	0.2859	193	0.2438	3669	3862	98
2.461-2.5034	0.3158	193	0.2464	3671	3864	99
2.5034-2.5489	0.3078	195	0.2363	3699	3894	98
2.5489-2.5979	0.2886	193	0.2303	3673	3866	98
2.5979-2.6509	0.279	192	0.2365	3646	3838	98
2.6509-2.7085	0.3095	194	0.2349	3681	3875	98
2.7085-2.7714	0.2868	194	0.2276	3680	3874	98
2.7714-2.8407	0.2662	191	0.2249	3637	3828	98
2.8407-2.9174	0.265	193	0.2158	3671	3864	97
2.9174-3.0032	0.2603	191	0.2165	3630	3821	97
3.0032-3.1	0.2757	193	0.2194	3662	3855	97
3.1-3.2107	0.2711	191	0.2032	3639	3830	97
3.2107-3.339	0.252	191	0.1949	3619	3810	96
3.339-3.4907	0.2123	190	0.1866	3608	3798	96
3.4907-3.6744	0.2095	192	0.169	3645	3837	96
3.6744-3.9041	0.2133	187	0.1585	3553	3740	95
3.9041-4.2047	0.174	189	0.147	3605	3794	95
4.2047-4.6263	0.1827	188	0.1386	3563	3751	94
4.6263-5.2922	0.1987	187	0.1507	3552	3739	94
5.2922-6.6541	0.1781	187	0.1667	3561	3748	93
6.6541-28.8772	0.1884	182	0.1491	3438	3620	89

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	3.4783	1.8345	-0.7318	1.8912	-0.9985	1.9154	0.1998	-0.1588	0.2808	0.2615	-0.1247	0.5767	-0.2881	-0.1583	-0.0753	0.3509	-0.1095	0.0778	0.4281	-0.0003	0.5274	11.3696	6.3006	27.7087
2	3.4829	1.939	0.0818	2.7952	-0.2456	2.1785	-0.0279	0.3841	0.0609	-0.1315	0.0778	0.523	-0.0394	-0.2582	-0.0801	0.3261	-0.1004	-0.0046	0.4785	-0.0176	0.5552	7.2294	4.4723	18.4328
3	1.9789	0.7865	0.4591	1.0914	-0.1067	1.285	0.0305	0.041	-0.0928	0.1048	-0.0336	0.3833	-0.057	-0.1007	-0.0057	0.2772	-0.1238	0.0525	0.3181	-0.026	0.4419	15.4227	1.6792	24.9303
4	0.7655	-0.4245	0.0818	0.4036	-0.1289	0.6913	0.098	0.3223	-0.2797	0.0621	-0.0903	0.2896	0.0912	-0.0911	-0.0164	0.2854	-0.1621	0.0162	0.4382	-0.043	0.3973	21.8641	-11.0491	19.4009
5	1.2718	0.1136	-0.1471	1.927	-0.2218	0.6496	0.1498	0.2459	-0.0547	-0.1482	-0.192	0.1193	-0.0448	-0.0078	0.0437	0.2765	-0.1237	-0.0102	0.543	-0.0125	0.2105	32.9038	-7.8361	8.9252
6	0.5556	0.0663	0.0575	0.3808	-0.1397	0.0632	0.0766	0.0349	-0.0067	0.1333	-0.0695	0.0642	-0.0784	-0.0197	0.0058	0.3311	-0.1775	0.0293	0.4106	-0.0282	0.3543	21.9552	-7.6497	21.192
7	0.4829	-0.2847	-0.8381	0.1687	0.4932	1.4565	0.0087	0.2949	-0.0511	0.0514	0.0721	0.8568	-0.0172	-0.7577	-0.0714	0.4941	0.0168	-0.0045	0.8849	-0.0553	0.4981	21.4598	-7.8742	-0.5943
8	5.2385	0.8405	-0.5002	3.8349	-1.2382	2.2844	-0.0455	0.0561	-0.063	-0.0108	0.0593	0.1333	0.1336	-0.1964	-0.0196	0.2846	-0.15	0.0436	0.4322	-0.0455	0.6734	6.992	-11.4297	18.6369
9	2.4226	-0.3127	0.8076	0.7604	-0.4302	0.9405	-0.1323	-0.3377	-0.2059	0.3699	0.0925	0.1677	0.2029	-0.1375	0.0894	0.684	-0.1993	-0.0023	0.4227	0.074	0.3343	51.7545	-34.4823	48.6594
10	3.0256	-0.3645	-0.4991	1.7111	0.1848	1.4351	-0.0787	-0.0258	-0.4825	0.1753	-0.0203	0.0482	0.291	-0.0361	0.0969	0.6469	-0.2261	0.0014	0.3907	0.0646	0.4066	54.8503	-42.4588	43.2351
11	0.7177	0.2292	0.0165	0.827	0.1421	0.6247	0.0201	0.0498	-0.1483	0.1334	0.0085	-0.1626	0.2299	0.2004	0.0309	0.3758	-0.1996	-0.0192	0.3288	0.0736	0.321	60.4273	-27.2696	34.2988
12	1.232	0.2765	0.1234	1.7632	-0.3044	1.1871	-0.061	0.175	-0.0247	-0.1413	0.0545	0.0295	-0.0102	-0.0659	0.0497	0.3191	-0.1801	-0.0031	0.3968	0.0323	0.2602	46.9179	-25.0415	15.4488
13	2.332	0.285	0.0557	1.8273	0.3731	1.0619	-0.0393	0.2247	-0.0356	-0.1487	0.0632	-0.1245	-0.0286	0.0656	0.0406	0.3693	-0.2256	-0.0145	0.4751	0.061	0.2862	58.8982	-22.8714	19.7441
14	0.9809	0.4809	0.7658	1.0153	-0.1528	1.1665	-0.0254	-0.1063	0.0051	0.1637	-0.0325	-0.0142	-0.0089	-0.0816	0.0551	0.3813	-0.1962	-0.0507	0.3742	0.0475	0.3329	56.3285	-20.8572	39.1938
15	1.3644	0.2626	1.3326	1.7912	2.1298	6.5736	-0.0745	0.1609	-0.4909	-0.0479	-0.0005	-0.0563	0.7046	-0.0575	0.053	0.4852	-0.2685	-0.0288	0.4877	0.0844	0.4586	59.748	-34.1915	22.0298
16	6.4951	-1.3997	-2.5689	9.4468	0.1748	5.7887	-0.007	0.1969	-0.375	-0.2855	0.0294	-0.0362	0.3888	0.2167	-0.0242	0.4338	-0.1626	-0.0562	0.4121	0.1012	0.4386	68.5235	-37.1985	38.1076
17	2.2482	0.724	0.3403	1.221	0.0312	0.7418	-0.0003	0.0734	-0.3635	-0.0373	-0.0293	-0.0443	0.1082	0.1028	0.0148	0.3749	-0.2063	-0.023	0.3946	-0.0635	0.5535	37.2562	-41.8557	21.2625
18	3.0959	0.7492	-0.6548	1.4239	-0.3408	1.2104	0.0824	-0.3022	-0.3703	0.175	-0.139	0.1144	0.0814	0.014	0.031	0.4028	-0.2263	-0.0302	0.4662	0.0093	0.5806	33.4428	-44.9349	30.0737
19	0.7718	0.5371	0.0805	1.1992	-0.0548	0.864	-0.0224	-0.0097	-0.1943	0.0429	-0.0925	0.1087	0.0623	-0.0774	0.0157	0.292	-0.3617	0.0379	0.3623	-0.0245	0.4301	36.3435	-36.2945	23.7128
20	0.1803	0.2978	0.3093	1.0074	0.2703	0.6466	0.0827	-0.1345	-0.1017	0.2779	-0.0946	0.1978	0.0001	-0.0594	0.0431	0.4349	-0.2316	0.0498	0.4601	0.004	0.4017	27.7884	-26.922	35.1007
21	0.0776	-0.1887	0.0362	0.5981	0.1481	0.4458	0.0553	-0.1475	-0.1509	0.1413	-0.0868	0.0893	-0.0128	0.0411	0.0136	0.3335	-0.2578	0.0323	0.3204	-0.0131	0.3224	34.6156	-20.1966	29.0013
22	2.1268	0.8281	-0.5458	1.7731	-0.6101	1.5108	0.0604	-0.0519	-0.0806	0.1538	-0.0586	0.4111	-0.0109	-0.1728	-0.0634	0.3026	-0.2685	0.0342	0.3231	-0.0337	0.4248	25.2114	-23.4351	25.1667
23	0.913	0.0513	0.3213	1.0317	-0.1317	1.016	0.0316	-0.1323	-0.1261	0.2576	-0.0922	0.1556	0.0204	-0.0667	0.0014	0.4709	-0.2287	0.0311	0.3433	0.0189	0.328	34.0247	-20.6798	39.7373
24	1.206	-0.7211	0.6224	2.6027	-0.9892	1.3364	0.0881	-0.0729	-0.0886	0.3177	-0.1373	-0.0341	-0.1036	0.1388	0.0419	0.5707	-0.2807	-0.06	0.4438	0.0767	0.2725	46.647	-13.547	44.3473
25	1.6579	-0.1918	0.1256	1.0717	-0.8958	0.7536	0.0933	-0.1785	-0.1056	0.3179	-0.0481	0.0989	-0.1525	0.0252	0.0179	0.412	-0.2221	0.0461	0.4141	-0.0021	0.2873	32.6257	-15.4143	38.4754
26	1.6742	0.3184	0.2748	2.1151	-0.2325	1.471	0.0135	0.0512	-0.1754	0.0086	-0.0416	0.0703	0.0717	0.0055	0.003	0.2961	-0.1664	0.0168	0.3725	-0.0117	0.3364	34.6616	-24.8396	21.3025
27	1.6411	0.9031	1.2617	1.9278	1.8121	4.7615	0.2413	-0.4375	-0.1704	0.6351	-0.1537	0.1516	0.1936	-0.0464	-0.0641	0.5467	-0.3139	0.1492	0.432	0.0218	0.323	30.2278	-25.4857	42.4859
28	4.226	1.0137	0.7174	3.8804	-0.5683	4.8445	0.0426	-0.1493	-0.0651	0.106	-0.0445	0.3079	0.1716	-0.4339	0.0029	0.3296	-0.2557	0.0399	0.3799	0.0125	0.6398	19.9799	-36.1984	29.4289
29	3.0227	-1.4505	-0.023	2.4436	0.3843	0.9205	0.1297	0.3215	0.2478	-0.2658	-0.0754	-0.2866	-0.1249	0.2266	-0.0334	0.2894	-0.2846	-0.0073	0.4872	0.1451	0.5803	82.8299	-1.8604	17.3611
30	2.3638	-0.3691	0.5007	1.598	-0.3664	1.7198	0.034	-0.1408	0.1574	0.0495	-0.0273	-0.1927	-0.125	0.0961	-0.0391	0.2675	-0.431	-0.0772	0.463	0.1368	0.6698	87.2142	1.2308	26.1389
31	0.6137	0.2674	-0.1301	0.731	0.1967	0.5209	0.0117	-0.1053	0.0125	0.5948	-0.0835	-0.3749	0.1208	0.2346	0.0001	0.2202	-0.4146	-0.0945	0.2139	0.1127	0.4357	68.1162	-5.4899	33.2783
32	2.372	-1.9085	-2.4795	3.6967	2.5744	3.0866	0.1902	-0.2284	0.2868	0.1249	0.0432	-0.3466	-0.5804	0.345	-0.1523	0.5242	-0.231	-0.0817	0.452	0.0899	0.4526	71.7353	0.0362	43.1582
33	6.4148	1.6749	0.889	6.3806	2.042	5.971	0.0209	0.0438	-0.388	0.0115	0.2615	-0.4891	0.3194	0.3423	-0.2856	0.3028	-0.2496	-0.1761	0.4576	0.1255	0.5996	85.3373	-11.6512	35.0014
34	1.3875	-0.3295	1.1323	0.0831	-0.2716	0.9179	-0.012	-0.1858	0.1128	0.1272	0.0766	0.0088	-0.0177	-0.0855	-0.0502	0.4262	-0.2437	-0.0168	0.3525	0.032	0.5668	69.6836	21.6566	34.8081
35	1.3228	0.1839	0.1874	2.267	-0.6737	1.4294	0.0797	0.0553	0.0437	-0.0283	-0.0005	-0.2315	-0.0218	0.1123	-0.0134	0.3113	-0.2727	-0.005	0.5428	0.039	0.57	75.129	23.6991	26.308
36	0.9492	0.3466	-0.1279	1.9567	0.2949	0.6238	0.0419	-0.0416	0.2889	-0.0358	0.0126	-0.1673	-0.1013	0.0562	-0.1021	0.3045	-0.2576	-0.0531	0.3306	0.1147	0.4594	66.0833	18.7254	30.0614
37	0.3117	-0.0868	-0.1748	0.9324	0.7925	0.6903	0.064	0.1216	0.1307	-0.113	0.0067	-0.204	-0.0754	0.0738	-0.0962	0.3448	-0.1364	0.0278	0.4795	0.1076	0.4119	61.8027	16.7174	13.5686
38	0.3017	-0.1738	-0.2058	0.3464	0.4772	0.6625	0.0494	0.0541	0.1404	-0.0391	-0.0307	-0.249	0.0117	0.1203	0.023	0.3496	-0.2143	-0.0271	0.332	0.0935	0.302	55.6651	9.6606	19.9955
39	0.7349	-0.3063	-0.329	0.4707	0.4333	0.5869	0.059	0.127	0.2145	-0.134	-0.0628	-0.1709	-0.1914	0.0024	-0.0526	0.3298	-0.2562	-0.0022	0.3412	0.1744	0.3726	57.0779	13.7777	15.3963
40	4.4645	-0.4054	-0.0827	1.2895	-0.0768	1.0649	-0.0307	0.0819	-0.0395	-0.0484	0.0286	-0.2121	0.0189	0.0386	0.0085	0.3115	-0.156	-0.0022	0.4353	0.0539	0.3745	62.4699	-8.1274	12.139
41	0.953	-0.0907	-0.1901	0.4774	-0.1653	0.5198	0.0505	0.0956	0.1124	-0.0557	0.0338	-0.1826	-0.0293	0.0306	-0.0498	0.3217	-0.1561	0.0003	0.4143	0.0971	0.3241	55.8666	9.1088	16.8495
42	1.5389	-1.6753	-1.2001	4.5243	3.7149	3.7548	0.0186	0.2019	0.3353	-0.423	0.093	-0.6054	-0.3613	0.6114	-0.0736	0.452	-0.1181	0.0724	0.4978	0.1834	0.4935	66.8308	12.6237	8.1266
43	5.7884	-0.7265	-1.8505	4.056	0.156	4.5621	0.1734	0.0057	0.4047	-0.1657	0.0461	-0.0486	-0.4243	0.0033	-0.2148	0.5154	-0.2232	0.0579	0.4916	0.1591	0.6308	63.6675	29.562	16.972
44	2.0229	0.3952	-1.4811	3.888	-2.2984	2.1511	0.0965	0.3921	0.0043	-0.6776	-0.0968	0.2731	0.0693	-0.4036	0.0988	0.4252	0.0622	-0.0226	0.7201	0.0433	0.2775	26.8099	13.9757	0.4989
45	2.1991	0.6045	-0.389	4.2312	-0.2348	1.4024	0.0817	0.1259	0.2826	-0.0143	-0.1488	0.3822	-0.2256	-0.3314	-0.0182	0.3728	0.1261	0.0068	0.7479	0.0575	0.3045	21.773	21.2392	6.4974
46	0.9127	-0.2322	-0.2348	0.406	0.3231	1.4537	0.1554	0.1578	0.2421	0.0377	-0.1945	-0.0294	-0.2518	-0.1179	0.0029	0.3374	-0.117	0.0213	0.4363	0.1185	0.3131	36.7963	16.7389	15.0612
47	1.0966	0.1584	-0.3868	0.8503	-0.0163	1.4198	0.026	-0.0284	0.073	0.1389	-0.1449	0.016	-0.0875	-0.1114	0.0389	0.3462	-0.1712	0.0373	0.3957	0.0428	0.2687	34.9509	10.5517	31.3177
48	1.952	-0.4923	-1.2389	1.1048	0.8379	3.6993	0.1233	0.0052	0.1699	0.0692	-0.2457	0.0906	-0.2344	-0.293	0.0883	0.3289	-0.1376	0.0112	0.4274	0.0674	0.3417	34.0399	16.9293	21.715
49	4.4818	-0.9747	-2.8634	4.1701	2.3953	8.7571	0.1477	0.227	0.4625	-0.2972	-0.0358	-0.1645	-0.4455	0.0163	-0.1335	0.6208	-0.0397	0.0071	0.5556	0.216	0.4748	34.1458	29.864	11.1968
50	1.5321	-1.2661	-1.4631	1.037	1.2022	1.3945	0.0628	0.1829	0.1205	-0.2558	-0.0766	-0.0612	-0.1355	-0.012	-0.0391	1.1636	-0.3071	-0.0492	1.2084	0.0505	0.336	25.6996	11.5819	47.6431
51	2.2036	0.9606	0.7641	1.9528	-1.4965	2.4447	-0.0886	0.1283	0.05	-0.1164	-0.0896	-0.2583	0.039	0.4881	0.1474	0.9219	-0.5905	-0.0419	1.6474	0.0928	0.5235	36.1399	8.7778	59.3626
52	2.0701	0.9784	-0.6307	0.6384	-0.4703	4.4285	-0.0576	0.1434	0.2004	-0.0815	-0.0204	-0.1245	-0.1061	0.2341	0.0573	0.9385	-0.6518	-0.103	1.6003	0.1327	0.5094	31.9517	13.8775	54.4352
53	0.0764	0.1407	0.094	0.6708	-0.7354	2.3804	-0.1866	0.1755	0.1151	-0.1703	0.0892	-0.0801	0.1418	0.4497	0.054	0.8743	-0.4495	0.0054	1.2528	-0.0126	0.3028	26.4737	4.5624	63.1966
54	1.6078	0.1453	0.5383	0.5929	-0.1281	1.0992	-0.3532	0.3362	-0.1744	-0.1464	0.3021	-0.1511	0.1607	0.6866	0.088	0.8663	-0.2043	0.1167	0.8894	-0.1137	0.3303	20.6613	-3.4987	66.6298
55	0.7712	0.2721	0.3414	0.3844	0.1478	1.4796	-0.5361	0.1616	0.0559	-0.0595	0.1986	-0.1294	-0.0726	0.5194	0.1334	0.8399	-0.1229	-0.0292	0.6687	-0.0509	0.2964	18.7134	4.2579	77.5605
56	0.3632	0.1195	-0.0671	0.4338	1.0231	2.7962	-0.2674	0.1683	0.0814	-0.1237	0.1767	-0.5271	-0.0369	0.6469	0.0637	0.8753	-0.1914	-0.0302	1.1134	-0.1087	0.3753	31.1088	4.3511	76.9887
57	5.3812	1.069	2.219	3.5362	-1.2265	1.7528	0.087	0.443	-0.361	-0.1752	0.0324	-0.1217	0.4391	0.237	-0.1314	0.8547	0.0014	0.1344	1.3102	-0.099	0.6372	36.2195	-3.5617	59.6825
58	2.3752	-0.6751	-1.0546	1.4942	-0.3321	0.7736	-0.0687	-0.0349	-0.9185	0.0544	-0.0575	-0.1057	0.4225	0.0196	0.1652	1.0072	0.1955	-0.1826	0.5834	0.0277	1.4246	11.6954	-31.2425	81.7719
59	0.8168	-0.8448	0.2514	0.8784	-0.2609	0.0762	0.2506	0.2805	-0.5257	-0.1302	-0.1555	0.0489	0.3369	0.1512	-0.0731	1.299	0.08	-0.1946	0.8656	-0.306	1.5533	12.1561	-36.716	75.8155
60	1.0988	0.1537	0.2538	1.2458	-0.1302	1.5921	-0.0378	0.2941	-0.7426	-0.2419	0.1103	-0.2387	0.7	0.4842	-0.0398	0.9748	0.1218	0.0109	0.4976	-0.0412	1.1049	11.5314	-26.2175	79.0479
61	0.704	-0.2535	0.5482	0.5224	-0.0491	0.4659	0.0078	0.479	-0.6115	-0.4784	0.0573	-0.1317	0.7657	0.4106	-0.094	0.926	0.0908	0.0546	0.7089	-0.387	0.8245	11.8729	-21.0489	62.7174
62	0.7712	0.3661	0.1255	0.8053	-0.1514	1.4528	-0.0116	0.5167	-0.7636	-0.3882	0.128	-0.1949	0.5455	0.5474	-0.0924	0.6818	0.0388	0.1358	0.5732	-0.2444	0.5536	14.0276	-13.0288	69.8578
63	2.0937	0.0628	-0.0787	1.2066	-0.5835	0.9233	0.0073	0.3598	-0.5018	-0.1815	0.1283	-0.0156	0.352	0.2987	-0.1318	0.9009	-0.1889	0.075	0.646	-0.2794	0.5158	1.5863	-13.3383	60.2614
64	0.1134	0.282	-0.1519	0.6678	-0.3666	0.2024	-0.0509	0.3129	-0.4287	-0.0679	0.2626	0.081	0.4872	0.0675	-0.2697	0.8214	-0.0302	0.0775	0.6533	-0.2951	0.7501	8.4402	-19.0478	64.9605
65	3.2193	1.243	0.8417	3.572	1.5852	2.9128	0.1371	0.1059	-0.4042	0.1003	0.0672	-0.282	0.3044	0.2983	-0.2082	1.2574	0.3158	0.1003	1.0995	-0.2876	1.2499	22.308	-28.9095	65.8101
66	1.21	-1.0186	-0.5692	2.5024	0.1941	0.3155	-0.0558	0.0845	0.1657	-0.1025	0.1627	-0.0755	-0.1838	0.1391	-0.0369	1.2622	-0.3478	-0.4679	0.8449	0.019	0.8863	26.4465	27.9183	77.6588
67	1.7116	-0.2976	0.1882	0.8303	-1.0689	1.3998	-0.0286	0.2295	0.2661	-0.3939	-0.0008	-0.0119	-0.1707	0.0736	-0.0148	1.3311	-0.3026	-0.3814	0.972	0.0649	0.8985	27.7388	32.246	68.2874
68	0.3573	-0.0118	0.1448	0.2613	-0.0924	0.7976	-0.3229	0.2149	0.4847	-0.0194	0.1345	0.0247	-0.5018	0.091	0.2564	1.445	-0.3896	-0.5232	0.6772	0.1653	0.7343	15.3191	27.2833	69.7771
69	0.6705	-0.4054	0.0916	0.3423	-0.0745	1.0541	-0.3062	0.5304	0.7939	-0.0181	0.1708	-0.2358	-0.5214	0.0223	0.1802	1.5695	-0.4567	-0.7799	0.555	0.2699	0.3805	5.6735	21.4068	64.5943
70	0.0758	0.0654	0.0889	0.3979	0.3744	0.3644	0.0143	0.1021	0.143	-0.0438	0.0503	-0.2528	-0.0478	0.0865	-0.06	1.5244	-0.3609	-0.4132	0.954	0.2499	1.2519	14.0927	40.1943	69.6301

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1003:1027)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 1028:1057)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 1058:1083)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 1084:1147)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 1148:1198)	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 1199:1222)	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 1223:1239)	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 1240:1253)	A
9	X-RAY DIFFRACTION	9	chain 'E' and (resseq 1004:1027)	E
10	X-RAY DIFFRACTION	10	chain 'E' and (resseq 1028:1057)	E
11	X-RAY DIFFRACTION	11	chain 'E' and (resseq 1058:1159)	E
12	X-RAY DIFFRACTION	12	chain 'E' and (resseq 1160:1182)	E
13	X-RAY DIFFRACTION	13	chain 'E' and (resseq 1183:1198)	E
14	X-RAY DIFFRACTION	14	chain 'E' and (resseq 1199:1211)	E
15	X-RAY DIFFRACTION	15	chain 'E' and (resseq 1212:1237)	E
16	X-RAY DIFFRACTION	16	chain 'E' and (resseq 1238:1253)	E
17	X-RAY DIFFRACTION	17	chain 'F' and (resseq 1004:1027)	F
18	X-RAY DIFFRACTION	18	chain 'F' and (resseq 1028:1057)	F
19	X-RAY DIFFRACTION	19	chain 'F' and (resseq 1058:1084)	F
20	X-RAY DIFFRACTION	20	chain 'F' and (resseq 1085:1106)	F
21	X-RAY DIFFRACTION	21	chain 'F' and (resseq 1107:1122)	F
22	X-RAY DIFFRACTION	22	chain 'F' and (resseq 1123:1147)	F
23	X-RAY DIFFRACTION	23	chain 'F' and (resseq 1148:1169)	F
24	X-RAY DIFFRACTION	24	chain 'F' and (resseq 1170:1182)	F
25	X-RAY DIFFRACTION	25	chain 'F' and (resseq 1183:1198)	F
26	X-RAY DIFFRACTION	26	chain 'F' and (resseq 1199:1211)	F
27	X-RAY DIFFRACTION	27	chain 'F' and (resseq 1212:1239)	F
28	X-RAY DIFFRACTION	28	chain 'F' and (resseq 1240:1253)	F
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 1003:1027)	D
30	X-RAY DIFFRACTION	30	chain 'D' and (resseq 1028:1057)	D
31	X-RAY DIFFRACTION	31	chain 'D' and (resseq 1058:1211)	D
32	X-RAY DIFFRACTION	32	chain 'D' and (resseq 1212:1239)	D
33	X-RAY DIFFRACTION	33	chain 'D' and (resseq 1240:1253)	D
34	X-RAY DIFFRACTION	34	chain 'C' and (resseq 1003:1027)	C
35	X-RAY DIFFRACTION	35	chain 'C' and (resseq 1028:1057)	C
36	X-RAY DIFFRACTION	36	chain 'C' and (resseq 1058:1084)	C
37	X-RAY DIFFRACTION	37	chain 'C' and (resseq 1085:1106)	C
38	X-RAY DIFFRACTION	38	chain 'C' and (resseq 1107:1122)	C
39	X-RAY DIFFRACTION	39	chain 'C' and (resseq 1123:1169)	C
40	X-RAY DIFFRACTION	40	chain 'C' and (resseq 1170:1182)	C
41	X-RAY DIFFRACTION	41	chain 'C' and (resseq 1183:1211)	C
42	X-RAY DIFFRACTION	42	chain 'C' and (resseq 1212:1239)	C
43	X-RAY DIFFRACTION	43	chain 'C' and (resseq 1240:1253)	C
44	X-RAY DIFFRACTION	44	chain 'B' and (resseq 1003:1027)	A - B
45	X-RAY DIFFRACTION	45	chain 'B' and (resseq 1028:1057)	A - B
46	X-RAY DIFFRACTION	46	chain 'B' and (resseq 1058:1147)	A - B
47	X-RAY DIFFRACTION	47	chain 'B' and (resseq 1148:1198)	A - B
48	X-RAY DIFFRACTION	48	chain 'B' and (resseq 1199:1239)	A - B
49	X-RAY DIFFRACTION	49	chain 'B' and (resseq 1240:1253)	A - B
50	X-RAY DIFFRACTION	50	chain 'H' and (resseq 1005:1020)	H
51	X-RAY DIFFRACTION	51	chain 'H' and (resseq 1021:1041)	H
52	X-RAY DIFFRACTION	52	chain 'H' and (resseq 1042:1057)	H
53	X-RAY DIFFRACTION	53	chain 'H' and (resseq 1058:1106)	H
54	X-RAY DIFFRACTION	54	chain 'H' and (resseq 1107:1147)	H
55	X-RAY DIFFRACTION	55	chain 'H' and (resseq 1148:1211)	H
56	X-RAY DIFFRACTION	56	chain 'H' and (resseq 1212:1240)	H
57	X-RAY DIFFRACTION	57	chain 'H' and (resseq 1241:1253)	H
58	X-RAY DIFFRACTION	58	chain 'I' and (resseq 1003:1030)	I
59	X-RAY DIFFRACTION	59	chain 'I' and (resseq 1031:1057)	I
60	X-RAY DIFFRACTION	60	chain 'I' and (resseq 1058:1084)	I
61	X-RAY DIFFRACTION	61	chain 'I' and (resseq 1085:1106)	I
62	X-RAY DIFFRACTION	62	chain 'I' and (resseq 1107:1144)	I
63	X-RAY DIFFRACTION	63	chain 'I' and (resseq 1145:1198)	I
64	X-RAY DIFFRACTION	64	chain 'I' and (resseq 1199:1239)	I
65	X-RAY DIFFRACTION	65	chain 'I' and (resseq 1240:1253)	I
66	X-RAY DIFFRACTION	66	chain 'G' and (resseq 1004:1027)	G
67	X-RAY DIFFRACTION	67	chain 'G' and (resseq 1028:1057)	G
68	X-RAY DIFFRACTION	68	chain 'G' and (resseq 1058:1106)	G
69	X-RAY DIFFRACTION	69	chain 'G' and (resseq 1107:1240)	G
70	X-RAY DIFFRACTION	70	chain 'G' and (resseq 1241:1253)	G

-
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

-
Protein , 1 types, 9 molecules AEFDCBHIG

-
Non-polymers , 5 types, 443 molecules

-
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

-Protein , 1 types, 9 molecules AEFDCBHIG

-Non-polymers , 5 types, 443 molecules

-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

-
Protein , 1 types, 9 molecules AEFDCBHIG

-
Non-polymers , 5 types, 443 molecules

-
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