PDB-4elf: Structure-activity relationship guides enantiomeric preference am...

ID or keywords:

Entry

Database: PDB / ID: 4elf

Title

Structure-activity relationship guides enantiomeric preference among potent inhibitors of B. anthracis dihydrofolate reductase

Components

Dihydrofolate reductase

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / dihydrofolate reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Bourne, C.R. / Barrow, W.W.

Citation

Journal: Biochim.Biophys.Acta / Year: 2013
Title: Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase.
Authors: Bourne, C.R. / Wakeham, N. / Nammalwar, B. / Tseitin, V. / Bourne, P.C. / Barrow, E.W. / Mylvaganam, S. / Ramnarayan, K. / Bunce, R.A. / Berlin, K.D. / Barrow, W.W.

History

Deposition	Apr 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 13, 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 / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details / _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	4elf.cif.gz	587.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4elf.ent.gz	488.8 KB	Display	PDB format
PDBx/mmJSON format	4elf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4elf_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	4elf_full_validation.pdf.gz	3.1 MB	Display
Data in XML	4elf_validation.xml.gz	67.9 KB	Display
Data in CIF	4elf_validation.cif.gz	90.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/el/4elf ftp://data.pdbj.org/pub/pdb/validation_reports/el/4elf	HTTPS FTP

-
Related structure data

Related structure data	4elbC 4eleC 4elgC 4elhC 3fl8S 3elb 3ele 3fl9 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ele-6 4elh-7 4elh-3 4ele-1 4ele-3 4elg-3 4elh-5 4elg-1 4ele-5 4elb-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (9)

Deposited unit

A: Dihydrofolate reductase

B: Dihydrofolate reductase

C: Dihydrofolate reductase

D: Dihydrofolate reductase

E: Dihydrofolate reductase

F: Dihydrofolate reductase

G: Dihydrofolate reductase

H: Dihydrofolate reductase

hetero molecules

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

1

A: Dihydrofolate reductase

hetero molecules

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

2

B: Dihydrofolate reductase

hetero molecules

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

3

C: Dihydrofolate reductase

hetero molecules

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

4

D: Dihydrofolate reductase

hetero molecules

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

5

E: Dihydrofolate reductase

hetero molecules

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

6

F: Dihydrofolate reductase

hetero molecules

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

7

G: Dihydrofolate reductase

hetero molecules

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

8

H: Dihydrofolate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.270, 136.120, 168.460
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Dihydrofolate reductase Mass: 19615.453 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: A thrombin cut site was engineered between the C-terminus and the 6 x His tag Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2083, BA_2237, dfrA, DHFR, GBAA_2237 / Plasmid: pCR-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81R22, dihydrofolate reductase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-35I / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(3,3,3-trifluoropropyl)phthalazin-2(1H)-yl ]prop-2-en-1-one / (S,E)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-(3,3,3-trifluoropropyl)phthalazin-2(1H)-yl)pro p-2-en-1-one Mass: 540.537 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₇H₂₇F₃N₆O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 947 / 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: 2.49 Å³/Da / Density % sol: 50.68 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 16-22% PEG 3350, 0.2M CaCl2, 0.1M MES, +/- 3% glycerol , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2010 / Details: Osmic Blue multilayer optics
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.3→37 Å / Num. obs: 67586 / % possible obs: 95.8 % / Redundancy: 2.5 % / B_iso Wilson estimate: 25.1 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 10.5

-
Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHENIX	(phenix.refine: 1.7.2_869)	refinement
d*TREK		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3FL8

3fl8

Resolution: 2.3→31.552 Å / SU ML: 0.87 / σ(F): 1.34 / Phase error: 31.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2898	3412	5.06 %
R_work	0.2282	-	-
obs	0.2313	67478	95.65 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 31.2 Å² / k_sol: 0.33 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.9107 Å²	-0 Å²	-0 Å²
2-	-	-1.1314 Å²	0 Å²
3-	-	-	-8.7793 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→31.552 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11034	0	328	947	12309

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	11723
X-RAY DIFFRACTION	f_angle_d	1.197	15902
X-RAY DIFFRACTION	f_dihedral_angle_d	19.883	4485
X-RAY DIFFRACTION	f_chiral_restr	0.073	1602
X-RAY DIFFRACTION	f_plane_restr	0.006	2019

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 (%)
2.3-2.3329	0.4796	124	0.3593	2529	X-RAY DIFFRACTION	91
2.3329-2.3677	0.4425	149	0.3306	2525	X-RAY DIFFRACTION	92
2.3677-2.4047	0.4078	117	0.3343	2541	X-RAY DIFFRACTION	92
2.4047-2.4441	0.3962	130	0.3544	2587	X-RAY DIFFRACTION	93
2.4441-2.4862	0.4233	142	0.3287	2527	X-RAY DIFFRACTION	93
2.4862-2.5314	0.4271	143	0.3279	2598	X-RAY DIFFRACTION	94
2.5314-2.58	0.3533	135	0.3016	2596	X-RAY DIFFRACTION	94
2.58-2.6327	0.4121	138	0.3057	2608	X-RAY DIFFRACTION	94
2.6327-2.6899	0.3993	151	0.2862	2597	X-RAY DIFFRACTION	96
2.6899-2.7524	0.3551	157	0.2637	2684	X-RAY DIFFRACTION	96
2.7524-2.8212	0.3614	139	0.2606	2651	X-RAY DIFFRACTION	96
2.8212-2.8975	0.322	142	0.2413	2689	X-RAY DIFFRACTION	97
2.8975-2.9827	0.3087	141	0.2484	2723	X-RAY DIFFRACTION	97
2.9827-3.0789	0.3048	130	0.2316	2710	X-RAY DIFFRACTION	98
3.0789-3.1888	0.3181	131	0.2321	2739	X-RAY DIFFRACTION	98
3.1888-3.3163	0.3069	168	0.2327	2692	X-RAY DIFFRACTION	98
3.3163-3.4671	0.2804	143	0.231	2731	X-RAY DIFFRACTION	98
3.4671-3.6496	0.2836	135	0.235	2759	X-RAY DIFFRACTION	98
3.6496-3.8779	0.2912	134	0.2132	2780	X-RAY DIFFRACTION	98
3.8779-4.1767	0.2185	147	0.177	2773	X-RAY DIFFRACTION	99
4.1767-4.5959	0.1969	156	0.1538	2789	X-RAY DIFFRACTION	99
4.5959-5.2583	0.2017	163	0.1566	2796	X-RAY DIFFRACTION	98
5.2583-6.6148	0.2679	158	0.2164	2762	X-RAY DIFFRACTION	97
6.6148-31.5552	0.2413	139	0.2093	2680	X-RAY DIFFRACTION	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	1.6983	0.1628	-0.1086	3.3738	-0.8797	6.9733	0.1463	0.0143	0.3484	0.0788	-0.0587	-0.0533	-0.4004	0.3832	-0.1166	0.1663	-0.0449	-0.0071	0.1624	0.0143	0.2436	15.8813	-33.5205	-3.4433
2	3.9743	0.1833	0.0203	5.8701	2.7583	7.3253	0.006	0.0586	0.2825	-0.386	-0.1262	-0.3198	-0.7458	0.6304	0.1255	0.3642	-0.1016	0.036	0.3085	0.0419	0.3052	21.1453	-23.1809	-15.3414
3	0.9164	-0.2516	-0.6266	2.0983	-1.0947	4.4757	0.0473	0.1024	0.0074	-0.194	0.0953	0.4093	-0.025	-0.5277	-0.1442	0.1519	-0.0051	-0.0545	0.2648	-0.0034	0.2673	11.4836	-37.8601	-5.6646
4	6.2972	4.742	1.562	4.9346	3.235	3.5439	-0.906	-0.6015	0.0666	-1.5847	-0.0453	0.7918	-0.9658	-0.7691	0.8588	0.7624	0.0175	-0.2383	0.4828	-0.0838	0.4387	6.0108	-51.8666	-22.2683
5	3.5288	-0.4127	0.3048	1.4468	-0.6458	5.0412	0.0377	0.2228	-0.3981	-0.3321	0.0849	-0.1636	0.5103	0.2148	-0.1047	0.2953	0.0098	0.0334	0.1465	-0.0006	0.2841	12.2979	-0.9681	2.6462
6	5.0177	-0.2894	0.1905	4.8081	1.6163	6.8386	-0.2051	0.1241	-0.2834	-0.0148	-0.0484	-0.1988	0.3363	0.427	0.2459	0.2681	0.0479	0.0123	0.1753	0.0445	0.2519	17.0856	-11.2321	15.1473
7	0.9551	0.0344	0.9996	1.7921	-1.5455	4.5983	0.0449	0.0185	0.0231	0.0136	-0.0034	0.2469	0.1413	-0.2435	-0.0464	0.1696	0.0107	0.0369	0.2325	0.0131	0.2898	8.0447	3.6257	4.7884
8	7.529	-9.5875	-7.7393	2.0176	2.0072	2.0061	-0.7289	-0.5248	-0.3004	0.4228	0.3385	0.7896	-0.2857	-0.2951	0.529	0.5874	0.0517	0.1176	0.4685	-0.1438	0.5035	4.763	17.4592	20.5807
9	2.4052	-0.2081	-1.4335	1.6508	-0.8944	6.0014	-0.031	-0.1735	-0.0087	0.2065	0.1037	-0.0987	-0.1218	-0.2653	-0.086	0.3898	0.0694	-0.067	0.2348	-0.003	0.2416	19.2929	-38.2707	39.2011
10	3.7811	0.0726	-1.7016	3.9303	0.0617	5.4469	-0.0982	-0.1328	0.2897	0.4127	0.0809	0.4161	-0.5883	-0.4432	0.0138	0.3383	0.1003	0.0147	0.2461	0.0151	0.3343	9.8435	-31.7083	26.6005
11	0.9186	0.3465	1.1032	0.3239	-0.0991	2.8544	0.0353	0.0288	-0.145	0.2821	0.0668	-0.0108	0.2173	0.0829	-0.0861	0.4356	0.0925	-0.028	0.2124	-0.0193	0.2847	24.3638	-41.5137	35.8279
12	5.4705	-0.402	-1.5248	5.3918	1.99	9.2468	-0.3896	-0.0665	-0.5956	1.1889	0.2807	0.7534	0.4657	-0.5684	0.1158	0.7063	-0.1443	0.2007	0.3492	-0.0216	0.4331	42.3857	-48.9451	18.1958
13	3.0015	0.1021	0.3102	2.6503	-0.9495	7.8228	-0.0751	-0.1419	0.504	0.1189	-0.1187	-0.2025	-0.6944	0.4834	0.1224	0.2616	-0.04	-0.0686	0.2244	0.0318	0.2905	12.024	33.4538	-3.4278
14	2.7755	-0.8528	-1.4057	6.0415	0.929	4.5822	0.0515	-0.2292	0.2761	0.0073	-0.1025	-0.4823	-1.0964	0.6595	0.0793	0.5541	-0.1352	-0.0413	0.2939	0.0397	0.3676	16.8249	43.7944	-15.7758
15	1.0775	-0.3042	1.223	1.6688	-1.3781	6.5975	-0.1649	-0.1013	0.0325	-0.0095	0.0285	0.202	-0.3641	-0.606	0.1492	0.1561	0.0089	-0.0186	0.2404	0.0141	0.2462	7.6753	28.9026	-5.6548
16	2.0039	2.0028	9.7206	2.0071	2.0027	2.0149	1.0336	1.871	-2.6963	0.0545	0.3426	-0.0385	1.472	0.032	-1.3061	0.769	-0.022	-0.2016	0.9496	-0.3233	0.9095	4.4865	14.5903	-22.204
17	2.4862	0.1937	0.4365	4.7182	-1.4555	7.0658	0.0962	-0.0935	-0.0211	-0.007	0.1143	0.58	-0.3782	-0.6698	-0.2133	0.2554	0.069	-0.0359	0.2452	0.0191	0.2523	14.126	28.0123	39.9538
18	2.7038	-0.1586	-1.0626	2.529	1.1318	4.0317	-0.0954	0.1159	0.3437	-0.091	-0.0125	0.4266	-1.1354	-0.8883	0.1367	0.626	0.2534	-0.0519	0.4754	-0.0109	0.3948	5.4005	34.6582	27.1939
19	1.7984	-0.0231	0.9434	0.9547	-0.8138	4.1054	0.0274	0.0179	-0.1425	0.1503	0.0298	-0.0199	-0.1837	-0.0541	-0.0667	0.3141	0.0251	-0.0312	0.148	-0.0108	0.2323	19.8727	26.0244	36.1192
20	6.2796	1.4494	2.7334	1.8682	-1.6395	4.5414	-0.43	-0.3581	-0.8821	0.761	0.3041	0.7315	0.101	-0.6333	0.1597	1.0157	0.195	0.1148	0.313	-0.0647	0.6795	37.772	20.5331	18.2978
21	1.3208	-0.5446	0.9405	3.7629	-1.0573	5.6402	0.0299	-0.1363	-0.048	0.2592	-0.0878	0.544	0.0251	-0.5408	-0.0415	0.2656	-0.0124	0.0264	0.4009	-0.0967	0.3538	-17.4876	-5.4225	40.7255
22	3.5097	0.2218	-1.2124	2.9925	0.3116	5.7175	-0.024	-0.185	0.4868	0.205	-0.0741	0.37	-0.6998	-0.7031	0.1006	0.3288	0.1001	-0.0427	0.375	-0.0948	0.3356	-25.4329	-1.7179	27.9098
23	3.0597	0.9262	-0.1377	3.0913	0.4575	6.5702	-0.0987	0.0481	-0.4085	-0.0795	-0.1671	-0.0021	0.5255	-0.1528	0.2412	0.2126	0.0217	0.0285	0.2051	-0.0301	0.2669	-10.1602	-8.4887	40.456
24	6.9408	2.8768	-0.2969	1.5566	-2.1968	2.0083	-0.8571	-0.6391	-0.0258	1.0985	0.259	1.6542	0.8046	-1.4317	0.5612	0.4357	0.0814	0.174	0.5031	0.0176	0.5221	3.1784	-13.9159	19.2876
25	4.9437	1.1079	-0.9276	1.7642	-1.1208	6.126	-0.1192	-0.0372	0.434	0.3161	0.0199	-0.1097	-0.5976	-0.162	0.0475	0.3152	-0.0432	-0.0825	0.1551	-0.0145	0.2622	-21.5623	-0.2414	-1.6145
26	3.8921	-2.0352	-0.1792	4.9805	0.4233	5.1293	-0.5806	-0.0526	0.2986	0.2966	-0.0055	-0.1089	-1.2494	0.4357	0.5359	0.5786	-0.1477	-0.2132	0.3085	0.0663	0.431	-17.0784	9.8153	-9.0625
27	0.9046	-0.8035	0.6248	1.4995	-1.071	5.0817	-0.0831	0.0573	0.1887	-0.0821	-0.1804	0.1021	-0.3697	-0.0724	0.2363	0.1869	-0.057	-0.0647	0.2387	-0.0065	0.2963	-22.6532	-1.3409	-8.6046
28	9.3629	1.2496	0.4041	6.2761	5.3607	8.7871	-0.1581	0.1204	1.158	1.4032	-0.2567	-0.0837	-1.8625	-0.2939	0.3907	0.7591	-0.044	-0.1608	0.408	-0.0327	0.4078	-29.0475	-22.5132	-24.0347
29	4.5759	1.1969	1.2033	3.9823	-2.2986	9.0599	-0.3063	0.0011	0.1091	0.1803	0.135	-0.4663	-0.4882	0.6628	0.091	0.2685	-0.0004	-0.0027	0.2412	0.0076	0.2665	17.5012	-3.0794	45.3233
30	3.133	-2.2316	0.0453	2.0569	-1.4251	7.1973	-0.602	0.3449	0.5513	0.4914	0.0508	-1.7936	-1.7431	2.298	0.4727	0.6965	-0.2812	-0.2443	1.0264	-0.0265	0.9647	30.46	0.8138	53.9282
31	3.8134	-1.1576	2.0947	2.274	-1.4398	8.5023	-0.2257	-0.5032	-0.0149	0.1823	0.0918	-0.2583	0.2129	0.0177	0.1069	0.2636	0.0126	0.042	0.1804	-0.0125	0.2519	13.4231	-6.2523	49.4048
32	4.4439	1.7812	-3.7052	1.0684	-1.0726	3.7556	-0.471	-0.6073	-0.9917	0.827	-0.1098	0.5697	0.7552	1.0379	0.5459	0.6812	0.0748	0.3346	0.627	0.1482	0.5933	-0.7177	-10.69	65.1615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:39)
2	X-RAY DIFFRACTION	2	(chain A and resid 40:91)
3	X-RAY DIFFRACTION	3	(chain A and resid 92:158)
4	X-RAY DIFFRACTION	4	(chain A and resid 159:166)
5	X-RAY DIFFRACTION	5	(chain B and resid 1:39)
6	X-RAY DIFFRACTION	6	(chain B and resid 40:91)
7	X-RAY DIFFRACTION	7	(chain B and resid 92:158)
8	X-RAY DIFFRACTION	8	(chain B and resid 159:166)
9	X-RAY DIFFRACTION	9	(chain C and resid 1:36)
10	X-RAY DIFFRACTION	10	(chain C and resid 37:90)
11	X-RAY DIFFRACTION	11	(chain C and resid 91:161)
12	X-RAY DIFFRACTION	12	(chain C and resid 162:166)
13	X-RAY DIFFRACTION	13	(chain D and resid 1:39)
14	X-RAY DIFFRACTION	14	(chain D and resid 40:91)
15	X-RAY DIFFRACTION	15	(chain D and resid 92:158)
16	X-RAY DIFFRACTION	16	(chain D and resid 159:166)
17	X-RAY DIFFRACTION	17	(chain E and resid 1:33)
18	X-RAY DIFFRACTION	18	(chain E and resid 34:90)
19	X-RAY DIFFRACTION	19	(chain E and resid 91:161)
20	X-RAY DIFFRACTION	20	(chain E and resid 162:166)
21	X-RAY DIFFRACTION	21	(chain F and resid 1:36)
22	X-RAY DIFFRACTION	22	(chain F and resid 37:109)
23	X-RAY DIFFRACTION	23	(chain F and resid 110:160)
24	X-RAY DIFFRACTION	24	(chain F and resid 161:166)
25	X-RAY DIFFRACTION	25	(chain G and resid 1:37)
26	X-RAY DIFFRACTION	26	(chain G and resid 38:65)
27	X-RAY DIFFRACTION	27	(chain G and resid 66:161)
28	X-RAY DIFFRACTION	28	(chain G and resid 162:166)
29	X-RAY DIFFRACTION	29	(chain H and resid 1:43)
30	X-RAY DIFFRACTION	30	(chain H and resid 44:82)
31	X-RAY DIFFRACTION	31	(chain H and resid 83:158)
32	X-RAY DIFFRACTION	32	(chain H and resid 159:166)

-
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