PDB-4fw3: Crystal Structure of the LpxC in complex with N-[(2S)-3-AMINO-1-(...

ID or keywords:

Entry

Database: PDB / ID: 4fw3

Title

Crystal Structure of the LpxC in complex with N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE inhibitor

Components

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

Keywords

Hydrolase/Hydrolase Inhibitor / Hydrolase / Hydrolase-Hydrolase Inhibitor complex

Function / homology

Function and homology information

UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding / membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Kang, Y.N. / Stuckey, J.A.

Citation

Journal: to be published
Title: Crystal Structure of the LpxC
Authors: Kang, Y.N. / Stuckey, J.A.

History

Deposition	Jun 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2	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.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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4fw3.cif.gz	481.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4fw3.ent.gz	397.6 KB	Display	PDB format
PDBx/mmJSON format	4fw3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4fw3_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4fw3_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4fw3_validation.xml.gz	45.4 KB	Display
Data in CIF	4fw3_validation.cif.gz	63.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fw/4fw3 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fw3	HTTPS FTP

-
Related structure data

Related structure data	4fw4C 4fw5C 4fw6C 4fw7C 3p3eS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4fw6-3 4fw7-4 4fw4-4 7ci9-d 7cia-d 7k9a-1 6mod-d 7cib-d 5n8c-1 4fw5-2 6i49-1 5upg-d 7ci8-2 4fw7-3 4ga8-d 4okg-1 3p3e-d 4p6w-d 3g59-d 1b02-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) 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

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

C: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

D: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

1

A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

2

B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

3

C: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

4

D: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	35.599, 170.903, 89.853
Angle α, β, γ (deg.)	90.000, 90.010, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / Protein envA / UDP-3-O-acyl-GlcNAc deacetylase Mass: 33418.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: envA, lpxC, PA4406 / Plasmid: pMOCR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI References: UniProt: P47205, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-L52 / N-[(2S)-3-amino-1-(hydroxyamino)-1-oxopropan-2-yl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide Mass: 347.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₁₇N₃O₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.04 Å³/Da / Density % sol: 39.85 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.9 Details: 24-30% PEG8000, 0.2M Sodium Acetate, 0.1M Sodium acetate pH 4.9, vapor diffusion, sitting drop, temperature 293.15K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2011

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.35→50 Å / Num. obs: 44503 / % possible obs: 99.9 % / Redundancy: 3.8 % / R_merge(I) obs: 0.116 / Χ²: 1.058 / Net I/σ(I): 5.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.35-2.39	3.8	0.452	2225	0.714	1	100
2.39-2.43	3.8	0.418	2200	0.732	1	100
2.43-2.48	3.8	0.394	2233	0.758	1	100
2.48-2.53	3.9	0.38	2239	0.769	1	100
2.53-2.59	3.8	0.339	2178	0.798	1	100
2.59-2.65	3.8	0.294	2229	0.792	1	100
2.65-2.71	3.8	0.266	2237	0.806	1	100
2.71-2.79	3.8	0.243	2197	0.842	1	100
2.79-2.87	3.8	0.216	2206	0.895	1	100
2.87-2.96	3.8	0.19	2278	0.927	1	99.8
2.96-3.07	3.8	0.165	2180	0.941	1	100
3.07-3.19	3.8	0.136	2230	1.007	1	100
3.19-3.33	3.8	0.126	2235	1.09	1	100
3.33-3.51	3.8	0.112	2223	1.377	1	99.9
3.51-3.73	3.8	0.105	2216	1.593	1	99.8
3.73-4.02	3.8	0.099	2244	2.041	1	99.9
4.02-4.42	3.7	0.089	2233	2.136	1	99.6
4.42-5.06	3.6	0.062	2224	1.367	1	99.5
5.06-6.37	3.8	0.047	2214	0.742	1	99.9
6.37-50	3.8	0.04	2282	0.923	1	99.8

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
BUSTER-TNT	BUSTER 2.11.1	refinement
PDB_EXTRACT	3.11	data extraction
MD2		data collection
HKL-2000		data reduction
PHASER		phasing
BUSTER	2.11.1	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3P3E

3p3e

Resolution: 2.35→42.73 Å / Cor.coef. F_o:F_c: 0.9333 / Cor.coef. F_o:F_c free: 0.8974 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.638 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2466	2239	5.04 %	RANDOM
R_work	0.1966	-	-	-
obs	0.199	44467	99.78 %	-

Displacement parameters

B_iso max: 115.9 Å² / B_iso mean: 35.5905 Å² / B_iso min: 12.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.2139 Å²	0 Å²	-0.928 Å²
2-	-	-3.3698 Å²	0 Å²
3-	-	-	1.1559 Å²

Refine analyze

Luzzati coordinate error obs: 0.307 Å

Refinement step

Cycle: LAST / Resolution: 2.35→42.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9290	0	120	327	9737

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	4520	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	244	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	1536	HARMONIC	5
X-RAY DIFFRACTION	t_it	9672	HARMONIC	20
X-RAY DIFFRACTION	t_nbd	0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	1256	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	11170	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	9672	HARMONIC	2	0.008
X-RAY DIFFRACTION	t_angle_deg	13121	HARMONIC	2	0.94
X-RAY DIFFRACTION	t_omega_torsion				2.43
X-RAY DIFFRACTION	t_other_torsion				2.7

LS refinement shell

Resolution: 2.35→2.41 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2372	180	5.56 %
R_work	0.2057	3056	-
all	0.2075	3236	-
obs	-	-	99.78 %

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	1.2286	0.7967	1.1899	2.1042	-0.2916	0.0082	-0.0349	0.0304	-0.0932	0.092	0.0242	-0.2962	-0.0393	0.0455	0.0108	-0.0926	0.0645	-0.0422	-0.0077	-0.019	-0.013	21.4441	-0.102	0.7788
2	2.4183	-0.008	-1.1993	3.2736	0.483	2.4247	-0.0063	-0.1347	-0.1944	0.0268	-0.0956	0.0685	0.107	0.0529	0.1018	-0.0614	0.0336	-0.0068	-0.0378	0.0073	-0.022	14.0456	-4.7385	6.9297
3	0.159	-0.4471	0.1721	0.5053	-0.5821	0.9687	0.0109	-0.0773	0.0217	0.0242	0.0124	0.0267	-0.0551	0.0332	-0.0233	0.1554	0.0279	-0.0541	0.0072	0.0955	-0.0269	5.8867	9.098	12.7522
4	0.3363	-1.6342	-0.2747	1.0582	-0.4273	-0.0001	-0.021	-0.0697	-0.0873	0.0919	-0.0008	0.0788	0.0328	0.0158	0.0218	-0.033	0.027	0.029	0.0227	-0.0188	-0.1286	9.4478	3.2578	12.1448
5	3.1857	0.3369	0.9624	0.4348	0.2448	0.0003	0.015	-0.0685	-0.0092	0.0372	0.1255	-0.0519	-0.0251	0.0705	-0.1406	0.0121	0.0309	-0.0548	-0.0202	-0.0005	0.0015	21.4938	3.4588	3.4687
6	0.2982	1.3369	1.1558	0.8887	-1.8903	1.9503	-0.0023	0.0134	-0.0258	-0.0392	-0.0208	-0.0291	-0.0651	-0.0226	0.0231	-0.0018	0.0115	-0.0414	-0.0151	-0.0287	-0.0111	8.9701	5.1036	-12.9057
7	3.7082	-0.566	0.6127	4.5555	-1.3609	0.0653	-0.012	-0.1601	0.1593	0.0314	0.0856	0.0651	-0.0441	-0.0249	-0.0736	-0.1336	0.0599	-0.0011	-0.0162	0.0644	0.0233	8.002	24.505	2.2138
8	2.4926	0.386	1.1949	0.9509	-1.2944	0.0238	-0.0197	0.1012	0.1056	-0.1646	0.0404	-0.1023	-0.0196	0.0708	-0.0207	-0.0628	0.0243	0.0202	-0.1378	0.0124	0.0217	21.2009	21.2185	-1.1631
9	0.1189	0.1253	-0.1253	0.1735	1.3648	1.1549	-0.0005	-0.0668	-0.0165	0.0632	-0.0088	0.0666	-0.0004	-0.0285	0.0093	0.2148	-0.0775	-0.0339	0.0223	-0.1059	-0.0747	15.4789	18.7924	22.7979
10	0.9205	1.1202	2.78	0.28	0.1025	1.4615	0.0153	-0.0427	0.1061	0.0485	0.0264	0.0198	-0.051	0.0129	-0.0417	0.0705	0.006	-0.1451	-0.1196	-0.0692	0.0107	23.3841	21.2004	19.0909
11	0.9183	0.6357	0.3275	3.4574	1.2239	1.9909	0.0307	-0.0197	-0.0018	-0.0989	-0.0592	0.1763	-0.0507	0.0425	0.0285	-0.1052	0.0537	0.0048	-0.0201	0.0395	-0.0777	10.6415	16.3817	1.5733
12	0.2416	1.2802	-1.3065	0.0048	-1.3012	-0.0005	-0.0053	-0.0127	0.0243	-0.0453	0.0069	-0.0413	-0.0206	0.0812	-0.0016	-0.0167	-0.0489	-0.0789	0.0118	0.016	0.0188	16.487	7.1247	-17.1798
13	1.5177	-0.5265	-0.3505	0.6989	0.355	2.406	0.0133	0.1945	0.0374	-0.1021	-0.0671	-0.0044	-0.0181	-0.0201	0.0537	-0.039	0.0287	-0.0083	0.023	0.0454	-0.0624	-4.8998	57.94	-10.4645
14	1.4659	0.8882	-1.6797	2.2411	1.8382	0.8238	0.0009	0.1027	0.0494	-0.0171	-0.0129	-0.0191	-0.0985	0.0766	0.012	-0.0405	-0.0071	0.0142	0.0407	0.0348	-0.0668	6.4389	64.206	-8.2388
15	1.2229	-0.3993	-0.7022	0.0006	-0.4652	1.725	-0.0204	0.0312	0.0235	-0.2048	-0.0516	-0.0647	-0.1925	0.1194	0.072	-0.0237	0.0165	0.0066	0.0264	0.0153	-0.0402	-1.2467	58.3152	-3.1061
16	0.7432	-0.5656	1.1428	0.0516	-0.7127	0.7785	0.0027	0.0021	-0.0245	0.0119	-0.0057	0.0225	0.0179	-0.0101	0.0031	-0.0307	0.1013	0.0328	0.1284	-0.0239	-0.0729	-6.158	48.6313	-19.8983
17	1.5604	-1.0602	-1.3327	0.0313	-1.5451	0.01	-0.0033	-0.0233	0.0105	0.026	-0.0031	-0.0387	0.0214	0.0298	0.0065	0.0636	0.0739	0.0005	-0.0244	0.065	-0.0345	12.5988	40.0304	-6.1982
18	1.5558	-0.61	-1.9889	1.3654	0.1905	1.1653	0.0658	-0.1112	-0.1897	0.0858	-0.1147	0.0404	0.0234	0.0229	0.0488	-0.0139	0.0278	0.0176	-0.0014	0.0316	-0.0746	4.1232	40.7762	10.0269
19	1.2164	-1.3559	1.7504	0	-1.0848	2.2502	-0.0073	0.0187	-0.0591	-0.017	0.0387	0.0619	0.0901	-0.0248	-0.0314	-0.089	-0.0394	0.0399	0.0348	0.0047	-0.0418	-6.8803	47.6339	6.5835
20	0.7171	0.0571	0.5459	1.5194	1.7716	0.9371	-0.0119	0.032	0.0247	-0.0411	-0.0015	0.0133	-0.0633	0.0133	0.0134	-0.0047	0.0131	-0.01	0.1009	-0.0183	0.0035	1.6519	64.8771	19.4115
21	0.391	2.5479	-0.5987	2.2394	-0.3879	0.7844	0.0139	-0.0653	-0.019	0.1072	-0.0384	0.1286	-0.0434	-0.0389	0.0244	-0.026	0.0241	0.046	0.0835	-0.0072	-0.0392	-8.6887	57.6831	17.7826
22	0.0448	-0.7956	-0.0321	0.795	-0.0372	0.4299	0.0221	-0.0669	-0.0599	-0.1726	-0.0632	-0.0114	0.1733	0.0234	0.0411	-0.0453	0.0276	-0.0207	0.01	-0.014	-0.0356	2.4568	46.0742	4.6162
23	0.321	1.6478	-0.025	0.0156	-0.9368	1.1005	0.0118	-0.0182	0.0387	-0.0348	-0.0313	-0.0292	0.0392	0.0751	0.0195	-0.0804	0.0262	0.0081	0.048	-0.0038	0.0194	17.3406	45.525	-4.6688
24	0.7865	1.0789	1.4822	0	-1.111	0.3234	-0.005	0.007	-0.0024	-0.038	-0.0173	0.0756	0.0267	-0.0387	0.0222	0.0031	0.0274	0.0686	0.041	-0.0391	-0.0243	-0.3234	36.7153	-15.5517
25	0.7856	0.7157	0.0175	0	1.0128	0.4957	-0.0009	0.0345	0.0499	-0.0221	0.0163	-0.0478	-0.0432	0.0133	-0.0153	0.0622	0.0089	0.0768	0.0282	0.0451	-0.0432	1.8602	7.2256	24.7244
26	0.1229	0.1772	0.6837	0.5069	0.2571	0.7119	0.0383	0.1558	0.0112	-0.0111	-0.0999	-0.0207	0.0505	-0.0279	0.0616	-0.068	0.043	0.0334	0.0559	-0.0054	-0.0511	5.5969	-13.5027	36.7556
27	3.494	0.2767	2.4393	1.5443	-0.9323	0.8176	0.0194	0.0866	-0.0533	-0.076	0.0209	-0.0072	0.0662	-0.0566	-0.0403	-0.0552	-0.0215	0.0168	0.0496	-0.0251	-0.0531	-6.3957	-15.8503	36.6822
28	0.9187	-0.9751	0.5769	0.1451	0.1808	1.8704	0.0147	0.063	-0.1389	-0.155	-0.1146	0.037	0.2033	-0.0673	0.0999	-0.0476	0.0097	0.0043	0.0189	-0.0269	-0.0192	1.5685	-9.634	41.2078
29	0.7168	-0.7447	1.4123	1.9949	0.033	0.0069	0.0039	0.1065	0.0044	0.019	0.0009	-0.0156	-0.026	0.0607	-0.0048	0.0567	0.0676	0.0018	-0.0034	-0.0179	-0.1051	-5.1351	6.0738	29.3764
30	1.7684	0.3849	-0.6358	0.2525	-0.7074	-0.0002	0.0218	-0.004	0.0355	0.0259	-0.0243	-0.0246	0.0011	-0.0196	0.0026	-0.0195	-0.0255	-0.0696	0.0881	-0.0881	0.0165	-17.1078	5.6468	51.8581
31	0.6534	-0.955	0.5455	1.4836	0.4013	0.5162	0.0052	-0.1216	0.1612	0.0731	0.0238	-0.1432	-0.2162	0.0355	-0.029	-0.0586	-0.003	-0.0021	0.0043	0.0138	-0.0813	-0.1875	6.1132	53.6645
32	0.8377	-0.4113	0.0766	1.8032	-2.1075	1.5098	-0.0068	0.027	-0.0305	-0.0273	0.0064	-0.0156	0.0442	0.0034	0.0004	0.0259	0.0012	0.0024	0.096	0.0079	-0.0309	-1.6771	-16.5546	64.3166
33	0.2025	1.3533	-0.3288	2.0418	1.5772	2.0077	0.0087	-0.0389	-0.0033	0.1292	-0.0106	-0.1477	0.0249	0.0053	0.0019	-0.0179	0.0229	-0.0288	0.1325	0.0284	-0.0696	8.5403	-9.493	62.7473
34	0.425	-1.2923	-1.204	0.967	0.0448	-0.0004	0.0034	-0.0258	0.1042	-0.1062	-0.0581	-0.0311	-0.0993	-0.0997	0.0547	-0.0671	0.0039	0.0086	0.0112	0.0063	-0.0386	-2.2617	2.2193	49.6921
35	1.2974	1.258	-0.8436	0	-0.3624	0.8094	0.012	-0.0174	-0.0291	-0.043	-0.034	0.0465	-0.0679	-0.0635	0.0219	-0.0851	0.0422	-0.006	0.0734	-0.0265	0.0063	-17.348	2.8281	40.2722
36	1.189	0.9076	-1.679	0.0071	1.8684	0.5484	-0.0072	0.0246	0.0084	-0.0451	-0.0089	-0.083	-0.0119	0.0519	0.0161	-0.0413	0.0213	-0.0604	0.0819	0.0334	-0.0316	0.3195	11.6196	29.4943
37	-0.0001	-0.5762	0.2259	0.4864	-0.0382	0.0001	-0.002	0.0148	-0.0699	-0.0882	0.0251	0.053	0.0369	-0.0626	-0.0231	-0.0196	0.0198	0.0426	-0.0121	0.0499	-0.0218	15.1845	50.471	33.3649
38	0.5658	0.3623	0.8636	2.5376	1.1595	1.3116	0.0087	-0.0754	0.1859	0.1598	-0.0301	0.0935	0.0899	-0.0829	0.0214	-0.0849	0.115	0.0795	0.0541	-0.0083	0.0351	15.6875	49.5328	53.5397
39	2.467	1.4419	0.4771	0	-0.6418	2.7827	-0.0165	-0.0541	0.0823	0.0165	-0.0384	-0.0924	-0.0354	0.032	0.0549	-0.0084	0.0005	0.0066	-0.0657	-0.0026	-0.0091	26.5071	51.8095	54.7397
40	1.6105	-0.3914	2.0202	0.0541	1.3007	1.2864	-0.0014	-0.0155	0.0129	0.058	-0.002	-0.0426	0.0674	-0.0387	0.0034	0.081	0.0083	-0.0135	-0.0269	-0.0395	-0.0939	28.4111	41.5841	57.53
41	3.6425	0.1324	-1.7526	2.1273	-1.0024	0.1997	-0.0034	-0.1373	0.0048	0.1078	0.0741	0.0296	-0.0769	-0.0357	-0.0707	-0.0102	0.032	0.049	-0.0208	-0.0118	-0.0241	16.5564	44.4857	51.0747
42	0.0223	-1.3798	-0.09	0.0672	0.1655	1.3177	-0.0079	0.0634	-0.0019	-0.0615	0.0303	0.0256	0.0024	0.0257	-0.0224	-0.0053	0.0383	0.0417	-0.0701	0.0107	-0.0187	21.5614	46.3297	32.9573
43	2.0639	-0.4223	0.9559	0.4041	1.1784	0.1642	0.0019	0.0208	-0.0462	-0.028	-0.0026	-0.0423	0.0106	0.0354	0.0006	-0.0016	0.05	0.0537	-0.0689	-0.0247	0.1013	36.3579	27.0706	44.3739
44	3.2356	0.596	-0.1833	3.4783	1.8524	-0.0001	-0.0015	-0.0924	-0.119	0.0899	0.0202	0.0463	0.0828	0.0142	-0.0186	-0.1029	0.0945	0.0143	-0.0254	-0.0273	-0.0225	22.6125	22.3299	47.2023
45	3.2594	0.5443	-2.1529	5.4661	-0.6906	0.6068	0.0263	-0.0005	-0.1557	0.1013	-0.0763	0.1529	0.0344	0.0097	0.0501	-0.059	0.0288	0.0443	-0.0962	-0.0109	-0.0637	15.6607	29.1044	52.3351
46	2.4421	-0.2757	-2.1372	0.8033	-0.5015	2.9278	0.0124	-0.0837	-0.0955	0.0907	0.033	-0.0423	0.0346	0.0735	-0.0454	0.1035	0.0564	0.1402	-0.0965	0.0267	0.0027	14.3755	29.1097	65.6095
47	0.5045	-0.3292	0.1883	2.2728	-0.5532	1.1384	-0.0055	-0.0577	0.0004	-0.0943	0.0174	-0.167	0.1082	-0.0133	-0.0119	-0.089	0.0505	0.0144	-0.0102	-0.0373	-0.069	25.1584	32.0191	46.3405
48	0.3765	1.6792	1.1148	0.0762	1.1087	0.0004	-0.0023	0.0035	-0.0106	-0.0534	0.0013	0.0557	0.0271	-0.0556	0.0009	0.0557	-0.0182	0.1262	0.0293	-0.0045	-0.0634	19.1176	41.2117	27.6991

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|-2 - 22}	A	-2 - 22
2	X-RAY DIFFRACTION	2	{A\|23 - 55}	A	23 - 55
3	X-RAY DIFFRACTION	3	{A\|56 - 63}	A	56 - 63
4	X-RAY DIFFRACTION	4	{A\|64 - 78}	A	64 - 78
5	X-RAY DIFFRACTION	5	{A\|79 - 120}	A	79 - 120
6	X-RAY DIFFRACTION	6	{A\|121 - 133}	A	121 - 133
7	X-RAY DIFFRACTION	7	{A\|134 - 167}	A	134 - 167
8	X-RAY DIFFRACTION	8	{A\|168 - 189}	A	168 - 189
9	X-RAY DIFFRACTION	9	{A\|190 - 205}	A	190 - 205
10	X-RAY DIFFRACTION	10	{A\|206 - 222}	A	206 - 222
11	X-RAY DIFFRACTION	11	{A\|223 - 282}	A	223 - 282
12	X-RAY DIFFRACTION	12	{A\|283 - 299}	A	283 - 299
13	X-RAY DIFFRACTION	13	{B\|-1 - 36}	B	-1 - 36
14	X-RAY DIFFRACTION	14	{B\|37 - 59}	B	37 - 59
15	X-RAY DIFFRACTION	15	{B\|60 - 116}	B	60 - 116
16	X-RAY DIFFRACTION	16	{B\|117 - 124}	B	117 - 124
17	X-RAY DIFFRACTION	17	{B\|125 - 138}	B	125 - 138
18	X-RAY DIFFRACTION	18	{B\|139 - 178}	B	139 - 178
19	X-RAY DIFFRACTION	19	{B\|179 - 193}	B	179 - 193
20	X-RAY DIFFRACTION	20	{B\|194 - 204}	B	194 - 204
21	X-RAY DIFFRACTION	21	{B\|205 - 227}	B	205 - 227
22	X-RAY DIFFRACTION	22	{B\|228 - 267}	B	228 - 267
23	X-RAY DIFFRACTION	23	{B\|268 - 282}	B	268 - 282
24	X-RAY DIFFRACTION	24	{B\|283 - 299}	B	283 - 299
25	X-RAY DIFFRACTION	25	{C\|-1 - 5}	C	-1 - 5
26	X-RAY DIFFRACTION	26	{C\|6 - 36}	C	6 - 36
27	X-RAY DIFFRACTION	27	{C\|37 - 59}	C	37 - 59
28	X-RAY DIFFRACTION	28	{C\|60 - 120}	C	60 - 120
29	X-RAY DIFFRACTION	29	{C\|121 - 132}	C	121 - 132
30	X-RAY DIFFRACTION	30	{C\|133 - 142}	C	133 - 142
31	X-RAY DIFFRACTION	31	{C\|143 - 193}	C	143 - 193
32	X-RAY DIFFRACTION	32	{C\|194 - 204}	C	194 - 204
33	X-RAY DIFFRACTION	33	{C\|205 - 226}	C	205 - 226
34	X-RAY DIFFRACTION	34	{C\|227 - 267}	C	227 - 267
35	X-RAY DIFFRACTION	35	{C\|268 - 282}	C	268 - 282
36	X-RAY DIFFRACTION	36	{C\|283 - 299}	C	283 - 299
37	X-RAY DIFFRACTION	37	{D\|-2 - 10}	D	-2 - 10
38	X-RAY DIFFRACTION	38	{D\|11 - 38}	D	11 - 38
39	X-RAY DIFFRACTION	39	{D\|39 - 59}	D	39 - 59
40	X-RAY DIFFRACTION	40	{D\|60 - 68}	D	60 - 68
41	X-RAY DIFFRACTION	41	{D\|69 - 117}	D	69 - 117
42	X-RAY DIFFRACTION	42	{D\|118 - 131}	D	118 - 131
43	X-RAY DIFFRACTION	43	{D\|132 - 145}	D	132 - 145
44	X-RAY DIFFRACTION	44	{D\|146 - 172}	D	146 - 172
45	X-RAY DIFFRACTION	45	{D\|173 - 201}	D	173 - 201
46	X-RAY DIFFRACTION	46	{D\|202 - 222}	D	202 - 222
47	X-RAY DIFFRACTION	47	{D\|223 - 282}	D	223 - 282
48	X-RAY DIFFRACTION	48	{D\|283 - 299}	D	283 - 299

-
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