PDB-4bnn: Crystal structure of S. aureus FabI in complex with NADP and 2-(2...

ID or keywords:

Entry

Database: PDB / ID: 4bnn

Title

Crystal structure of S. aureus FabI in complex with NADP and 2-(2- cyanophenoxy)-5-hexylphenol

Components

ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

Keywords

OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / SAFABI

Function / homology

Function and homology information

enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / : / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding / identical protein binding
Similarity search - Function

Biological species

STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Schiebel, J. / Chang, A. / Bommineni, G.R. / Tonge, P.J. / Kisker, C.

Citation

Journal: Biochemistry / Year: 2013
Title: Rational Optimization of Drug-Target Residence Time: Insights from Inhibitor Binding to the S. Aureus Fabi Enzyme-Product Complex.
Authors: Chang, A. / Schiebel, J. / Yu, W. / Bommineni, G.R. / Pan, P. / Baxter, M.V. / Khanna, A. / Sotriffer, C.A. / Kisker, C.F. / Tonge, P.J.

History

Deposition	May 15, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 5, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	4bnn.cif.gz	835.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4bnn.ent.gz	701.1 KB	Display	PDB format
PDBx/mmJSON format	4bnn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4bnn_validation.pdf.gz	4.6 MB	Display	wwPDB validaton report
Full document	4bnn_full_validation.pdf.gz	4.7 MB	Display
Data in XML	4bnn_validation.xml.gz	93.1 KB	Display
Data in CIF	4bnn_validation.cif.gz	122.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/4bnn ftp://data.pdbj.org/pub/pdb/validation_reports/bn/4bnn	HTTPS FTP

-
Related structure data

Related structure data	4bnfC 4bngC 4bnhC 4bniC 4bnjC 4bnkC 4bnlC 4bnmC 4alkS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4d41-1 4d43-1 6yur-2 4alk-2 4alk-1 4ali-1 4bng-1 4d42-1 6tbc-2 4bni-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
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (2) #235 - Jul 2019 AMPA Receptor similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

hetero molecules

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

1

E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

hetero molecules

defined by author&software
129 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

hetero molecules

defined by author&software
129 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.920, 94.600, 94.270
Angle α, β, γ (deg.)	97.92, 111.96, 97.31
Int Tables number	1
Space group name H-M	P1

#1: Protein	ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH] / ENR / ENOYL-ACP REDUCTASE Mass: 31144.240 Da / Num. of mol.: 8 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria) Strain: N315 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7A6D8, UniProt: A0A0H3JLH9*PLUS, EC: 1.3.1.10
#2: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#3: Chemical	ChemComp-JUS / 2-(2-CYANOPHENOXY)-5-HEXYLPHENOL Mass: 295.376 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₉H₂₁NO₂
#4: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1038 / 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: 2.9 Å³/Da / Density % sol: 58 % / Description: NONE
Crystal grow	pH: 6.5 / Details: 0.1 M NA/K-PHOSPHATE PH 6.5, 45% MPD

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.25→40.9 Å / Num. obs: 129530 / % possible obs: 97.5 % / Observed criterion σ(I): 6 / Redundancy: 2 % / R_merge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shell	Resolution: 2.25→2.37 Å / Redundancy: 2 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / % possible all: 96.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ALK

4alk

Resolution: 2.25→40.9 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.943 / SU B: 12.791 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20612	6528	5 %	RANDOM
R_work	0.15128	-	-	-
obs	0.15402	122997	97.53 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 34.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.12 Å²	0.19 Å²	0.21 Å²
2-	-	-1.81 Å²	-0.99 Å²
3-	-	-	-1.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→40.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15675	0	620	1038	17333

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	17054
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.761	2.009	23093
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.119	5	2131
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.024	24.837	767
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.61	15	2981
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.162	15	106
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	2579
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	12750
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.296	1.5	10360
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.104	2	16601
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.737	3	6694
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.577	4.5	6469
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.31	443	-
R_work	0.241	9075	-
obs	-	-	96.76 %

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	2.8371	0.4261	-0.8012	3.8686	-0.1527	0.5895	-0.2025	-0.4539	-0.3122	0.3347	0.1758	-0.2345	0.0567	0.261	0.0266	0.13	0.0655	-0.0432	0.2639	0.0706	0.1121	12.712	32.9831	19.9661
2	4.5829	0.7078	0.0133	0.9429	0.464	2.5551	-0.0301	-0.7503	-0.3221	0.2481	-0.0175	-0.097	0.2939	0.2497	0.0476	0.178	0.0902	0.025	0.2449	0.1471	0.1419	8.7698	29.1903	27.0693
3	1.0302	0.0647	-0.1294	1.4297	-0.0317	0.6648	-0.17	-0.3368	-0.1214	0.2287	0.1006	0.1329	-0.0875	0.0601	0.0694	0.1627	0.0265	0.0264	0.2019	0.0484	0.1144	-0.8844	38.7262	22.3877
4	1.2561	0.0138	0.3858	0.7027	0.4754	1.1492	-0.0535	-0.1665	-0.0144	0.1345	0.0541	0.0643	-0.0286	0.0087	-0.0006	0.1395	-0.0025	-0.0098	0.1492	0.032	0.1414	-3.1769	42.0524	11.4386
5	0.9365	-0.2195	-0.5976	0.5425	-0.4299	1.0771	-0.0575	-0.1274	-0.0464	0.0747	0.1018	0.0333	-0.1009	0.0169	-0.0443	0.2147	0.0045	0.0083	0.146	0.0025	0.1581	2.9775	44.0025	8.112
6	5.4406	0.3755	-4.3424	6.9709	4.2601	7.8444	-0.6169	0.507	-0.6351	0.1471	0.1443	0.3149	0.7986	-0.7188	0.4727	0.163	-0.0759	-0.0184	0.1718	0.0148	0.3508	1.753	23.4961	1.2509
7	1.6817	0.2843	-0.7767	1.1036	-0.1791	0.5188	-0.0423	-0.0956	-0.107	0.0397	0.0161	-0.0402	-0.0187	0.129	0.0262	0.0868	-0.0041	-0.0161	0.1827	0.0213	0.1765	13.6498	36.003	4.1834
8	2.0569	0.1172	-0.2133	2.9976	0.086	2.6613	-0.0072	0.3372	0.207	-0.1096	0.0311	0.1836	-0.4149	-0.4026	-0.0239	0.231	0.1672	-0.0202	0.1831	0.022	0.1028	-22.9725	58.0343	-11.4268
9	2.16	0.0712	0.4933	2.3999	2.3601	7.2113	0.2305	0.2273	0.1968	-0.1874	-0.2366	0.2966	-0.5681	-0.7698	0.0061	0.204	0.2147	-0.0344	0.243	0.0091	0.2193	-30.0444	60.208	-6.821
10	2.3674	-0.1528	0.662	0.6574	0.5434	1.3645	0.013	-0.0269	-0.0381	0.0111	-0.0901	0.2471	-0.3542	-0.3759	0.0771	0.2663	0.1168	0.0313	0.2377	0.0016	0.2177	-24.5258	50.0174	0.9085
11	1.4807	0.119	0.3955	0.6234	0.4961	1.8421	0.0052	0.0285	-0.0427	0.0817	0.0262	0.0947	-0.1556	-0.2031	-0.0314	0.1138	0.0638	0.0022	0.1204	0.0058	0.1712	-13.066	47.838	2.4308
12	1.1847	-0.7647	-0.0919	0.5878	-0.2852	1.2858	0.0126	0.0452	-0.0033	0.0419	-0.0043	0.001	-0.2403	-0.1581	-0.0083	0.1945	0.0289	0.0079	0.1508	0.0178	0.1687	-9.5785	47.3604	-3.4184
13	9.1995	2.7657	-4.9476	4.3931	0.2924	6.7202	0.5146	-0.4945	0.5871	0.1674	-0.1939	-0.0173	-1.1858	0.1856	-0.3207	0.4458	0.0436	-0.0108	0.0493	-0.0205	0.223	-4.4589	68.2366	-0.2571
14	1.135	0.0784	-0.1297	1.9098	0.6189	1.3209	0.0573	0.1631	0.1108	-0.1314	-0.0254	0.0439	-0.2914	-0.088	-0.0319	0.2646	0.0395	0.0094	0.1101	0.0295	0.0911	-6.5985	56.8602	-12.9218
15	4.2911	0.7602	-2.1086	1.925	0.4656	1.4333	0.09	0.6941	0.0528	-0.3376	-0.1473	0.2087	-0.2353	-0.4358	0.0573	0.2853	0.0787	-0.0761	0.3638	0.027	0.062	-4.8654	50.3464	-34.37
16	7.1598	-4.4071	-1.5641	3.8007	2.6025	3.0055	0.2402	0.5657	0.1396	-0.4539	-0.3089	-0.0047	-0.4628	-0.3284	0.0687	0.2522	-0.003	-0.019	0.4094	0.0559	0.0137	-1.688	49.4805	-42.4902
17	1.0246	-0.0379	0.1173	1.4662	0.5635	2.0169	0.0041	0.3355	0.0898	-0.0975	0.0377	-0.0748	-0.3513	0.1148	-0.0418	0.3171	0.0042	0.0796	0.2385	0.0496	0.0871	9.997	52.3804	-34.5504
18	1.6585	-0.5673	0.5682	1.254	-0.0919	0.9942	0.0592	0.1986	0.0898	-0.1437	0.0132	-0.0363	-0.2301	0.0471	-0.0724	0.2333	-0.0336	0.0292	0.1506	0.0023	0.0625	12.2624	49.2675	-23.8361
19	0.7295	-0.1135	-0.2828	0.3185	0.5913	1.4155	0.0137	0.1871	-0.0069	-0.0871	-0.021	-0.0114	-0.1999	0.0721	0.0073	0.2004	-0.0271	0.0058	0.1456	0.0191	0.1348	6.8887	50.4977	-19.536
20	9.5016	2.8618	-4.8348	3.2271	-2.9365	5.3101	-0.4317	0.3277	-0.8928	-0.2461	0.0404	-0.0856	0.5668	0.06	0.3913	0.1606	0.0043	-0.0021	0.1268	-0.1005	0.2521	1.133	30.0788	-23.6325
21	1.7029	-0.1716	-0.7629	0.6409	-0.29	0.6605	0.0108	0.2209	-0.0268	-0.0751	-0.0566	-0.0579	-0.1118	-0.1489	0.0458	0.2687	0.0414	-0.0193	0.1811	-0.0229	0.1161	-5.9544	45.2723	-19.176
22	2.3347	1.3277	0.0276	2.3535	2.086	2.7301	-0.0484	-0.314	-0.1625	-0.0808	0.2359	-0.3194	-0.0906	0.4639	-0.1875	0.0273	-0.0207	-0.0616	0.403	-0.0977	0.303	34.0718	45.3688	2.2946
23	7.8379	2.0087	-0.9073	0.6317	0.3507	4.1759	0.0942	-0.2116	-0.12	-0.0182	0.0874	-0.1667	-0.5412	0.9512	-0.1815	0.1109	-0.0837	-0.0852	0.4488	-0.1329	0.3773	42.1527	46.8309	-1.1277
24	2.3064	-0.8225	0.6073	2.2574	-0.2057	2.7266	-0.0372	0.0214	0.099	-0.1361	0.1433	-0.251	-0.0876	0.5223	-0.1061	0.0396	-0.1001	0.0154	0.3366	-0.0852	0.2662	33.9562	44.3469	-12.5166
25	1.6662	-0.535	0.3569	0.6037	-0.4127	1.3084	0.1165	0.0501	-0.0169	-0.1173	0.0653	-0.0623	-0.2698	0.3948	-0.1818	0.2051	-0.1351	0.0395	0.2659	-0.0644	0.1857	22.896	46.2981	-13.9528
26	1.4433	0.2569	0.3631	3.9204	-0.4618	1.6161	-0.0276	-0.0218	0.273	0.1946	0.0572	-0.2192	-0.3811	0.1105	-0.0297	0.1141	-0.0587	-0.0069	0.235	-0.0124	0.1929	19.7128	51.1409	-6.1731
27	1.0245	-0.0483	-0.3342	1.2895	0.1033	1.8245	-0.01	-0.1317	0.0467	-0.089	0.0633	-0.0173	-0.0639	0.2398	-0.0533	0.0857	-0.043	-0.0405	0.1734	-0.0293	0.1471	18.4245	47.8563	4.3259
28	3.9618	1.0579	-1.9578	2.4803	0.8436	3.77	-0.0296	0.3771	0.0055	-0.2229	-0.1048	0.3112	-0.3836	-0.2693	0.1344	0.2153	0.0506	-0.0844	0.1005	0.0087	0.1496	-32.3972	17.7089	8.5362
29	3.7604	2.0043	1.0818	5.056	0.1112	3.7252	-0.1621	-0.0919	0.2978	-0.8039	-0.1851	0.362	-0.5308	-0.1936	0.3471	0.2624	0.063	-0.1422	0.1021	0.0376	0.2135	-31.8716	26.304	7.2734
30	1.7876	-0.4699	0.2964	1.7022	-0.0672	1.2187	-0.0292	0.0182	0.2441	-0.1064	-0.0584	0.1317	-0.3882	-0.0419	0.0876	0.201	0.0077	-0.0212	0.0888	0.0193	0.1711	-27.3538	24.5372	20.6064
31	1.8232	-0.3822	0.5338	1.0543	0.1264	0.9743	0.0308	-0.1034	0.0455	-0.0727	-0.048	0.0569	-0.1904	-0.026	0.0172	0.1438	-0.0039	0.0262	0.1103	0.0211	0.1494	-21.3183	15.3879	25.0083
32	2.812	0.0701	-0.6472	1.568	0.2613	2.2973	-0.0421	0.291	0.0091	-0.1409	0.0089	-0.1431	-0.2049	0.1371	0.0332	0.1161	-0.0209	-0.0167	0.1567	0.0118	0.193	-19.6531	9.1843	17.8639
33	1.6009	0.1626	-0.2549	1.4527	0.2671	1.8351	-0.0987	0.1105	-0.1246	-0.0623	-0.006	0.1609	-0.0657	0.018	0.1047	0.0824	-0.0156	-0.0253	0.141	-0.0095	0.16	-26.0314	2.8331	11.3498
34	2.1185	-1.8722	-0.9948	4.0047	1.0942	3.5639	-0.0925	-0.3065	-0.0441	0.5469	0.1374	-0.1424	0.1465	0.2355	-0.0449	0.2641	0.0328	-0.0695	0.1537	-0.0048	0.0242	-2.5867	1.606	49.9843
35	4.4911	-3.5749	-0.3551	5.9109	2.5004	2.5908	-0.0909	-0.1766	0.1752	1.1123	0.1019	-0.3984	0.3754	0.3269	-0.011	0.5631	-0.0529	-0.1761	0.2872	0.0387	0.0685	-0.778	8.0814	55.4518
36	2.861	-0.1749	0.6885	1.0452	0.6312	1.4995	-0.1203	-0.2066	0.1574	0.2246	0.1572	-0.1641	-0.1273	0.1843	-0.037	0.2389	-0.0177	-0.014	0.1591	-0.0211	0.0957	-4.3337	14.7315	43.5141
37	1.0825	-0.3136	0.3992	1.251	0.3677	0.8164	-0.0068	-0.0148	0.0017	0.1103	0.0121	-0.0179	-0.0674	0.0633	-0.0053	0.1548	-0.0191	0.0238	0.1625	0.0033	0.0941	-12.3603	11.1102	35.5615
38	1.2477	-0.7234	-0.7123	0.9269	0.2211	2.6236	0.022	-0.0107	0.03	0.1729	0.0083	-0.0184	0.0077	0.0165	-0.0302	0.1347	-0.0263	-0.0014	0.1327	-0.0005	0.1464	-11.1508	4.5939	33.5915
39	6.4036	1.3693	-2.0345	13.0714	1.5394	0.9602	0.1293	-0.3612	0.3039	0.9822	-0.2474	1.3688	0.101	0.0273	0.1181	0.3886	0.0194	0.1589	0.415	0.0482	0.1839	-25.9643	-0.0921	48.3281
40	0.703	0.3674	-0.4098	1.135	0.4171	0.9078	-0.0362	-0.0614	-0.0482	0.2638	0.0208	0.0052	0.2205	0.0961	0.0154	0.206	0.0184	0.0154	0.1642	0.0265	0.1365	-12.2483	-7.2481	40.4917
41	2.2702	0.0719	-0.0205	2.8476	2.2573	1.8173	0.0383	-0.0965	-0.3219	0.437	0.1651	-0.2894	0.368	0.2113	-0.2035	0.2298	0.0912	-0.0764	0.2186	0.0344	0.2345	0.6645	-24.7105	34.6682
42	1.6422	-1.4738	0.3437	3.7395	2.509	4.7666	-0.2705	-0.2792	-0.269	0.3741	0.3288	-0.334	0.2827	0.2121	-0.0583	0.3982	0.1401	-0.0109	0.1619	0.0674	0.5435	3.0951	-32.9116	32.8216
43	1.6166	-0.5748	-0.1595	1.2568	0.2484	0.9033	0.0589	-0.0162	-0.4029	0.149	0.0118	0.0207	0.4675	0.0561	-0.0707	0.3271	0.0354	-0.0234	0.0559	0.0143	0.2608	-10.7553	-32.198	28.7629
44	0.9133	-0.3863	1.153	2.06	-0.5844	1.5607	0.0902	0.0017	-0.1627	0.2147	0.012	0.1422	0.2017	0.0098	-0.1022	0.1713	0.0228	0.0533	0.0824	0.003	0.2266	-16.6136	-23.55	24.5305
45	2.3176	-0.2729	-1.0207	0.9687	0.9356	1.8395	0.0489	0.0492	-0.1665	0.1482	-0.007	0.0924	0.2009	0.0085	-0.0419	0.1871	0.0069	0.0257	0.0857	0.0247	0.1858	-15.8321	-17.5966	28.3463
46	4.3915	5.6439	0.248	14.1433	-2.6567	3.0426	-0.2717	0.4503	-0.2853	-1.1769	0.3547	-0.611	0.0758	0.4328	-0.083	0.2519	0.0154	0.0792	0.3437	-0.0701	0.1995	-0.011	-13.2798	14.1498
47	0.3693	0.5823	0.4525	1.0331	0.758	0.8227	0.028	0.04	-0.111	0.1593	0.1011	-0.1395	0.1036	0.095	-0.1291	0.1255	0.0514	-0.0054	0.1998	0.0027	0.1627	-4.3535	-10.0434	30.5227
48	2.7299	-0.1416	-2.2255	2.8778	-1.4132	5.8175	-0.0124	0.3203	0.0602	-0.2787	-0.0671	0.6761	0.1385	-0.6219	0.0796	0.0685	-0.0528	-0.1041	0.2303	-0.0868	0.3513	-44.1622	-10.508	8.3314
49	6.169	0.5073	0.9267	6.5381	2.2002	0.8415	0.0228	-0.1527	-0.0986	-0.4732	-0.2712	0.7992	-0.1358	-0.1673	0.2484	0.1175	-0.0612	-0.1352	0.508	-0.1308	0.4763	-48.7508	-17.6443	5.6468
50	3.9405	-0.4034	1.607	2.3087	-1.9162	2.5539	0.1347	0.2676	-0.4025	-0.1055	-0.1447	0.2895	0.225	-0.0883	0.01	0.0869	-0.0793	-0.0485	0.2205	-0.1545	0.4692	-35.8012	-22.7986	8.4888
51	1.0754	-0.1281	0.8095	2.543	0.2202	0.7243	0.0865	0.0442	-0.1786	0.1103	-0.1028	0.3667	0.1552	-0.0601	0.0163	0.1482	-0.0736	0.055	0.1896	-0.0586	0.3529	-28.0127	-19.2483	15.9909
52	0.8936	0.1357	0.2513	1.6203	0.1672	0.09	0.0016	0.0351	-0.1669	0.0947	-0.0182	0.1231	0.0056	-0.0172	0.0166	0.0332	-0.0319	-0.0093	0.2033	-0.0431	0.2988	-26.9215	-12.6552	16.1775
53	1.9441	-0.6902	-3.0712	10.2584	1.1181	5.6503	-0.0191	0.0171	-0.1784	1.1134	-0.2057	0.6669	0.2808	-0.772	0.2247	0.2346	-0.2043	0.0541	0.7075	0.063	0.4725	-41.7937	-12.29	31.5526
54	0.4816	-0.064	-0.1033	2.658	-0.8554	0.7763	-0.0665	-0.0142	-0.0469	-0.0584	-0.0295	0.2839	0.0402	0.0091	0.096	0.0534	-0.0118	0.0022	0.2121	-0.0292	0.2868	-35.149	-2.1434	18.9522

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 29
2	X-RAY DIFFRACTION	2	A	30 - 61
3	X-RAY DIFFRACTION	3	A	62 - 104
4	X-RAY DIFFRACTION	4	A	105 - 154
5	X-RAY DIFFRACTION	5	A	155 - 193
6	X-RAY DIFFRACTION	6	A	194 - 214
7	X-RAY DIFFRACTION	7	A	215 - 256
8	X-RAY DIFFRACTION	8	B	3 - 29
9	X-RAY DIFFRACTION	9	B	30 - 61
10	X-RAY DIFFRACTION	10	B	62 - 104
11	X-RAY DIFFRACTION	11	B	105 - 154
12	X-RAY DIFFRACTION	12	B	155 - 193
13	X-RAY DIFFRACTION	13	B	194 - 214
14	X-RAY DIFFRACTION	14	B	215 - 256
15	X-RAY DIFFRACTION	15	C	3 - 29
16	X-RAY DIFFRACTION	16	C	30 - 61
17	X-RAY DIFFRACTION	17	C	62 - 104
18	X-RAY DIFFRACTION	18	C	105 - 154
19	X-RAY DIFFRACTION	19	C	155 - 193
20	X-RAY DIFFRACTION	20	C	194 - 214
21	X-RAY DIFFRACTION	21	C	215 - 256
22	X-RAY DIFFRACTION	22	D	3 - 29
23	X-RAY DIFFRACTION	23	D	30 - 61
24	X-RAY DIFFRACTION	24	D	62 - 104
25	X-RAY DIFFRACTION	25	D	105 - 154
26	X-RAY DIFFRACTION	26	D	155 - 214
27	X-RAY DIFFRACTION	27	D	215 - 256
28	X-RAY DIFFRACTION	28	E	3 - 29
29	X-RAY DIFFRACTION	29	E	30 - 61
30	X-RAY DIFFRACTION	30	E	62 - 104
31	X-RAY DIFFRACTION	31	E	105 - 154
32	X-RAY DIFFRACTION	32	E	155 - 214
33	X-RAY DIFFRACTION	33	E	215 - 256
34	X-RAY DIFFRACTION	34	F	3 - 29
35	X-RAY DIFFRACTION	35	F	30 - 61
36	X-RAY DIFFRACTION	36	F	62 - 104
37	X-RAY DIFFRACTION	37	F	105 - 154
38	X-RAY DIFFRACTION	38	F	155 - 193
39	X-RAY DIFFRACTION	39	F	194 - 214
40	X-RAY DIFFRACTION	40	F	215 - 256
41	X-RAY DIFFRACTION	41	G	3 - 29
42	X-RAY DIFFRACTION	42	G	30 - 61
43	X-RAY DIFFRACTION	43	G	62 - 104
44	X-RAY DIFFRACTION	44	G	105 - 154
45	X-RAY DIFFRACTION	45	G	155 - 193
46	X-RAY DIFFRACTION	46	G	194 - 214
47	X-RAY DIFFRACTION	47	G	215 - 256
48	X-RAY DIFFRACTION	48	H	3 - 29
49	X-RAY DIFFRACTION	49	H	30 - 61
50	X-RAY DIFFRACTION	50	H	62 - 104
51	X-RAY DIFFRACTION	51	H	105 - 154
52	X-RAY DIFFRACTION	52	H	155 - 193
53	X-RAY DIFFRACTION	53	H	194 - 214
54	X-RAY DIFFRACTION	54	H	215 - 256

-
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://pdbjlvh1.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