PDB-4fq9: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd...

ID or keywords:

Entry

Database: PDB / ID: 4fq9

Title

Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa

Components

3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

Keywords

LYASE / hot dog fold / fatty acid biosynthesis / bacterial virulence

Function / homology

Function and homology information

trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / : / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.02 Å

Authors

Moynie, L. / Mcmahon, S.A. / Duthie, F.G. / Naismith, J.H.

Citation

Journal: J.Mol.Biol. / Year: 2013
Title: Structural insights into the mechanism and inhibition of the beta-hydroxydecanoyl-acyl carrier protein dehydratase from Pseudomonas aeruginosa
Authors: Moynie, L. / Leckie, S.M. / McMahon, S.A. / Duthie, F.G. / Koehnke, A. / Taylor, J.W. / Alphey, M.S. / Brenk, R. / Smith, A.D. / Naismith, J.H.

History

Deposition	Jun 25, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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	4fq9.cif.gz	663.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4fq9.ent.gz	553.2 KB	Display	PDB format
PDBx/mmJSON format	4fq9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4fq9_validation.pdf.gz	514.3 KB	Display	wwPDB validaton report
Full document	4fq9_full_validation.pdf.gz	526.1 KB	Display
Data in XML	4fq9_validation.xml.gz	67.5 KB	Display
Data in CIF	4fq9_validation.cif.gz	92 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fq/4fq9 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/4fq9	HTTPS FTP

-
Related structure data

Related structure data	4b0bC 4b0cC 4b0iC 4b0jC 4b8uC C: citing same article (ref.)
Similar structure data	4cl6-3 4b0i-3 4b0c-3 1mka-d 5hd6-1 3fmu-d 4b0c-1 4zyl-d 4b0b-d 6kv9-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) 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.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (4)

Deposited unit

A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

F: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

G: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

H: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

I: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

J: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

hetero molecules

190 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

hetero molecules

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

2

C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

hetero molecules

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

3

E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

F: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

hetero molecules

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

4

G: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

H: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

hetero molecules

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

5

I: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

J: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

hetero molecules

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

Unit cell

Length a, b, c (Å)	146.790, 135.780, 111.010
Angle α, β, γ (deg.)	90.000, 108.820, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	A	A	2 - 171	3 - 172
2	1	PHE	PHE	B	B	2 - 171	3 - 172
1	2	PHE	PHE	A	A	2 - 171	3 - 172
2	2	PHE	PHE	C	C	2 - 171	3 - 172
1	3	PHE	PHE	A	A	2 - 171	3 - 172
2	3	PHE	PHE	D	D	2 - 171	3 - 172
1	4	PHE	PHE	A	A	2 - 171	3 - 172
2	4	PHE	PHE	E	E	2 - 171	3 - 172
1	5	PHE	PHE	A	A	2 - 171	3 - 172
2	5	PHE	PHE	F	F	2 - 171	3 - 172
1	6	PHE	PHE	A	A	2 - 171	3 - 172
2	6	PHE	PHE	G	G	2 - 171	3 - 172
1	7	PHE	PHE	A	A	2 - 171	3 - 172
2	7	PHE	PHE	H	H	2 - 171	3 - 172
1	8	SER	SER	A	A	2 - 170	3 - 171
2	8	SER	SER	I	I	2 - 170	3 - 171
1	9	PHE	PHE	A	A	2 - 171	3 - 172
2	9	PHE	PHE	J	J	2 - 171	3 - 172
1	10	PHE	PHE	B	B	2 - 171	3 - 172
2	10	PHE	PHE	C	C	2 - 171	3 - 172
1	11	PHE	PHE	B	B	2 - 171	3 - 172
2	11	PHE	PHE	D	D	2 - 171	3 - 172
1	12	PHE	PHE	B	B	2 - 171	3 - 172
2	12	PHE	PHE	E	E	2 - 171	3 - 172
1	13	PHE	PHE	B	B	2 - 171	3 - 172
2	13	PHE	PHE	F	F	2 - 171	3 - 172
1	14	PHE	PHE	B	B	2 - 171	3 - 172
2	14	PHE	PHE	G	G	2 - 171	3 - 172
1	15	PHE	PHE	B	B	2 - 171	3 - 172
2	15	PHE	PHE	H	H	2 - 171	3 - 172
1	16	SER	SER	B	B	2 - 170	3 - 171
2	16	SER	SER	I	I	2 - 170	3 - 171
1	17	PHE	PHE	B	B	2 - 171	3 - 172
2	17	PHE	PHE	J	J	2 - 171	3 - 172
1	18	PHE	PHE	C	C	2 - 171	3 - 172
2	18	PHE	PHE	D	D	2 - 171	3 - 172
1	19	PHE	PHE	C	C	2 - 171	3 - 172
2	19	PHE	PHE	E	E	2 - 171	3 - 172
1	20	PHE	PHE	C	C	2 - 171	3 - 172
2	20	PHE	PHE	F	F	2 - 171	3 - 172
1	21	PHE	PHE	C	C	2 - 171	3 - 172
2	21	PHE	PHE	G	G	2 - 171	3 - 172
1	22	PHE	PHE	C	C	2 - 171	3 - 172
2	22	PHE	PHE	H	H	2 - 171	3 - 172
1	23	SER	SER	C	C	2 - 170	3 - 171
2	23	SER	SER	I	I	2 - 170	3 - 171
1	24	PHE	PHE	C	C	2 - 171	3 - 172
2	24	PHE	PHE	J	J	2 - 171	3 - 172
1	25	PHE	PHE	D	D	2 - 171	3 - 172
2	25	PHE	PHE	E	E	2 - 171	3 - 172
1	26	PHE	PHE	D	D	2 - 171	3 - 172
2	26	PHE	PHE	F	F	2 - 171	3 - 172
1	27	PHE	PHE	D	D	2 - 171	3 - 172
2	27	PHE	PHE	G	G	2 - 171	3 - 172
1	28	PHE	PHE	D	D	2 - 171	3 - 172
2	28	PHE	PHE	H	H	2 - 171	3 - 172
1	29	SER	SER	D	D	2 - 170	3 - 171
2	29	SER	SER	I	I	2 - 170	3 - 171
1	30	PHE	PHE	D	D	2 - 171	3 - 172
2	30	PHE	PHE	J	J	2 - 171	3 - 172
1	31	PHE	PHE	E	E	2 - 171	3 - 172
2	31	PHE	PHE	F	F	2 - 171	3 - 172
1	32	PHE	PHE	E	E	2 - 171	3 - 172
2	32	PHE	PHE	G	G	2 - 171	3 - 172
1	33	PHE	PHE	E	E	2 - 171	3 - 172
2	33	PHE	PHE	H	H	2 - 171	3 - 172
1	34	SER	SER	E	E	2 - 170	3 - 171
2	34	SER	SER	I	I	2 - 170	3 - 171
1	35	PHE	PHE	E	E	2 - 171	3 - 172
2	35	PHE	PHE	J	J	2 - 171	3 - 172
1	36	PHE	PHE	F	F	2 - 171	3 - 172
2	36	PHE	PHE	G	G	2 - 171	3 - 172
1	37	PHE	PHE	F	F	2 - 171	3 - 172
2	37	PHE	PHE	H	H	2 - 171	3 - 172
1	38	SER	SER	F	F	2 - 170	3 - 171
2	38	SER	SER	I	I	2 - 170	3 - 171
1	39	PHE	PHE	F	F	2 - 171	3 - 172
2	39	PHE	PHE	J	J	2 - 171	3 - 172
1	40	PHE	PHE	G	G	2 - 171	3 - 172
2	40	PHE	PHE	H	H	2 - 171	3 - 172
1	41	SER	SER	G	G	2 - 170	3 - 171
2	41	SER	SER	I	I	2 - 170	3 - 171
1	42	PHE	PHE	G	G	2 - 171	3 - 172
2	42	PHE	PHE	J	J	2 - 171	3 - 172
1	43	SER	SER	H	H	2 - 170	3 - 171
2	43	SER	SER	I	I	2 - 170	3 - 171
1	44	PHE	PHE	H	H	2 - 171	3 - 172
2	44	PHE	PHE	J	J	2 - 171	3 - 172
1	45	SER	SER	I	I	2 - 170	3 - 171
2	45	SER	SER	J	J	2 - 170	3 - 171

NCS ensembles :

Details

biological unit is a dimer. There are 5 biological units in the asymmetric unit (chains A & B, chains C & D chains E & F, chains G & H and chains I & J

#1: Protein	3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase / Beta-hydroxydecanoyl thioester dehydrase Mass: 18825.586 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: fabA, PA1610 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: O33877, EC: 4.2.1.60
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.79 Å³/Da / Density % sol: 55.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 18% PEG 3350, 0.12M Sodium Potassium Phosphate, 6.4% Hexanediol,100mM Sodium citrate pH 4.5, vapour diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.9919 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.9919 Å / Relative weight: 1

Reflection

Resolution: 2.016→105.075 Å / Num. all: 133404 / Num. obs: 133404 / % possible obs: 98.6 % / Redundancy: 3.2 % / R_sym value: 0.082 / Net I/σ(I): 8.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.02-2.07	2.9	0.477	1.5	28543	9819	0.477	98.3
2.07-2.12	3	0.435	1.6	28372	9605	0.435	98.7
2.12-2.19	3	0.379	1.8	27712	9329	0.379	98.4
2.19-2.25	2.9	0.336	2.1	25737	9029	0.336	98.6
2.25-2.33	3.3	0.282	2.5	28784	8850	0.282	99
2.33-2.41	3.3	0.244	2.9	28181	8529	0.244	99.3
2.41-2.5	3.3	0.207	3.4	27434	8259	0.207	99.1
2.5-2.6	3.3	0.182	3.8	26114	7909	0.182	99.2
2.6-2.72	3.1	0.156	4.4	23827	7623	0.156	98.6
2.72-2.85	3.3	0.122	5.6	24228	7235	0.122	98.8
2.85-3.01	3.4	0.1	6.9	23407	6899	0.1	98.6
3.01-3.19	3.3	0.086	7.9	21896	6540	0.086	98.4
3.19-3.41	3.3	0.072	8.7	19727	6069	0.072	98.1
3.41-3.68	3.1	0.067	9.1	17297	5610	0.067	96.7
3.68-4.03	3.4	0.06	10	17686	5228	0.06	98.2
4.03-4.51	3.3	0.055	10.4	15978	4789	0.055	98.6
4.51-5.2	3.1	0.054	10.7	12874	4164	0.054	97.8
5.2-6.37	3.3	0.05	11.6	11851	3585	0.05	99
6.37-9.02	3.3	0.045	11.5	9103	2783	0.045	99.3
9.02-105.075	3.2	0.041	11.9	4959	1550	0.041	98.2

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
SCALA	3.3.16	data scaling
PHASER		phasing
REFMAC	5.6.0119	refinement
PDB_EXTRACT	3.11	data extraction
MxCuBE		data collection
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.02→105.075 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.751 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2108	6719	5 %	RANDOM
R_work	0.1866	-	-	-
obs	0.1878	133404	98.54 %	-

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 max: 108.03 Å² / B_iso mean: 38.1013 Å² / B_iso min: 20.69 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0 Å²	0.06 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.02→105.075 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13128	0	122	721	13971

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	13547
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	9322
X-RAY DIFFRACTION	r_angle_refined_deg	1.49	1.965	18314
X-RAY DIFFRACTION	r_angle_other_deg	1.403	3	22554
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.212	5	1693
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.204	23.178	601
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.602	15	2184
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.637	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1964
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	15195
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2933

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

LS refinement shell

Resolution: 2.016→2.068 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	489	-
R_work	0.269	9187	-
all	-	9676	-
obs	-	-	98.2 %

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	0.6792	0.2589	-0.0701	2.4426	0.2891	1.2498	-0.095	-0.1591	0.0628	0.0977	0.0164	0.5814	0.0134	-0.2316	0.0786	0.0285	0.0195	0.0346	0.1091	-0.0143	0.1566	-79.965	0.992	42.324
2	2.0462	2.4139	0.5225	7.3609	3.321	3.3147	-0.3439	0.1671	-0.194	-0.5667	0.3752	0.1779	-0.122	-0.0431	-0.0313	0.1023	0.0142	-0.0106	0.1317	-0.0022	0.1294	-74.081	-2.554	33.42
3	1.7401	-0.1828	0.5607	1.9127	0.4943	1.1714	-0.1236	-0.3187	-0.1354	0.3484	0.0709	0.0183	0.0522	-0.1545	0.0527	0.1296	0.0105	0.059	0.1431	0.0383	0.0786	-64.483	-14.824	51.217
4	2.6445	1.8349	2.02	8.2198	3.4104	4.3382	-0.2568	-0.0742	0.1944	0.1382	0.2188	-0.3506	-0.4575	0.1121	0.038	0.1198	0.0161	-0.0009	0.0977	0.0137	0.1349	-57.619	-6.895	46.7
5	1.1344	0.0255	-0.0978	0.698	-0.084	0.9166	-0.0242	0.0337	-0.0182	-0.0155	0.0213	0.0699	0.1703	-0.0398	0.0029	0.1013	-0.0454	-0.0049	0.0872	0.0115	0.1152	-58.687	-32.385	27.511
6	1.3334	-0.2173	-0.8103	2.0314	0.9052	6.5694	0.0734	0.2137	0.0745	-0.3158	-0.045	0.0036	-0.3804	-0.0641	-0.0284	0.0774	-0.0374	0.0077	0.162	0.0255	0.2125	-55.609	-23.345	21.599
7	1.1048	0.4521	-0.3117	1.0803	0.2164	1.1301	-0.0184	-0.115	-0.1205	0.1167	0.024	-0.1831	0.1704	0.1543	-0.0056	0.096	0.0229	-0.0184	0.0778	0.0196	0.1237	-34.845	-33.294	27.399
8	1.7642	0.1559	0.0689	2.2815	-0.2065	7.1333	0.0187	-0.4419	0.0067	0.3403	-0.0143	-0.0037	-0.4047	0.1075	-0.0044	0.0906	-0.0237	-0.0112	0.2043	0.0075	0.1763	-37.162	-23.436	32.387
9	2.519	4.244	-1.0775	7.2771	-1.8097	2.383	-0.3034	0.1262	0.1589	-0.6938	0.246	0.2944	-0.118	-0.113	0.0574	0.2485	-0.0245	-0.0613	0.1031	-0.046	0.1333	-33.649	-22.552	-7.308
10	0.9549	0.3228	0.0663	1.3865	0.0095	1.1704	-0.0107	0.0745	0.0255	-0.1241	-0.0006	0.0797	-0.0364	-0.0055	0.0113	0.083	-0.0021	0.0021	0.1016	-0.0165	0.1562	-29.519	-15.082	4.53
11	0.7165	0.2088	0.2007	2.1855	0.1243	0.8412	-0.004	0.076	-0.0539	0.0207	0.0636	-0.4151	-0.0297	0.2087	-0.0596	0.0059	-0.0171	0.0142	0.1261	-0.0111	0.1858	-11.755	-2.51	10.012
12	2.6366	-1.8609	0.8548	6.3398	-2.8719	3.8168	-0.1646	-0.2859	-0.3576	0.6568	0.363	-0.1086	-0.0985	-0.1618	-0.1984	0.1299	-0.0192	-0.045	0.1137	0.0071	0.1778	-17.413	-5.009	19.443
13	0.9137	-0.1154	0.2825	1.1125	0.3162	0.7635	0.026	0.0242	-0.0253	-0.1748	-0.0021	0.1669	-0.1242	0.0115	-0.0239	0.1065	-0.0526	0.0025	0.0859	0.0367	0.1078	-25.921	25.538	7.701
14	1.5014	-0.3735	0.6427	2.537	0.1245	1.4725	-0.1293	-0.1257	-0.1031	0.0108	0.0786	0.3723	-0.0811	-0.162	0.0507	0.1022	-0.0419	0.013	0.1333	0.0449	0.167	-28.633	19.864	15.463
15	0.8682	-0.0182	-0.084	1.412	0.3772	0.5177	-0.0169	-0.201	0.0617	0.1661	0.0036	0.0702	-0.0955	-0.0082	0.0134	0.1168	-0.0361	0.0314	0.1592	0.0146	0.0682	-19.742	32.98	30.957
16	5.6074	-0.4283	-0.2308	4.1143	0.2381	2.1267	0.0166	-0.2956	-0.8367	0.2786	-0.0127	-0.0264	0.1653	0.084	-0.0039	0.1753	-0.0589	0.0252	0.2298	0.0455	0.138	-19.313	21.712	32.8
17	1.1498	0.342	0.046	1.5709	-0.3089	1.7263	0.029	-0.0867	0.081	0.1045	0.0123	0.0391	-0.069	0.1308	-0.0413	0.0777	0.053	-0.0029	0.1096	-0.0562	0.0913	-64.352	26.465	42.339
18	6.2414	2.2423	-0.4782	3.1074	0.2264	1.7655	-0.0721	-0.032	-0.2919	-0.1609	0.0792	-0.4371	0.0176	0.4326	-0.0071	0.0902	0.0851	0.0029	0.2217	-0.0458	0.1325	-55.983	21.32	36.77
19	1.6472	0.0592	0.2262	1.6802	-0.6543	1.8718	-0.0173	0.1949	0.1753	-0.3457	0.0184	0.1171	-0.0759	0.1679	-0.0011	0.1142	0.0063	-0.027	0.0973	0.0139	0.0841	-67.363	34.647	20.188
20	5.8474	0.7729	-0.1245	4.2515	-0.902	3.5272	0.033	0.2614	-0.5909	-0.5822	0.0478	0.2271	0.373	-0.0264	-0.0808	0.2286	0.0438	-0.0616	0.1587	-0.0027	0.1166	-68.707	23.418	18.843

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 131
2	X-RAY DIFFRACTION	2	A	132 - 171
3	X-RAY DIFFRACTION	3	B	2 - 131
4	X-RAY DIFFRACTION	4	B	132 - 171
5	X-RAY DIFFRACTION	5	C	2 - 131
6	X-RAY DIFFRACTION	6	C	132 - 171
7	X-RAY DIFFRACTION	7	D	2 - 131
8	X-RAY DIFFRACTION	8	D	132 - 171
9	X-RAY DIFFRACTION	9	E	2 - 15
10	X-RAY DIFFRACTION	10	E	16 - 171
11	X-RAY DIFFRACTION	11	F	2 - 131
12	X-RAY DIFFRACTION	12	F	132 - 171
13	X-RAY DIFFRACTION	13	G	2 - 101
14	X-RAY DIFFRACTION	14	G	102 - 171
15	X-RAY DIFFRACTION	15	H	2 - 131
16	X-RAY DIFFRACTION	16	H	132 - 171
17	X-RAY DIFFRACTION	17	I	2 - 131
18	X-RAY DIFFRACTION	18	I	132 - 171
19	X-RAY DIFFRACTION	19	J	2 - 131
20	X-RAY DIFFRACTION	20	J	132 - 171

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi