PDB-2av9: Crystal Structure of the PA5185 protein from Pseudomonas Aerugino...

ID or keywords:

Entry

Database: PDB / ID: 2av9

Title

Crystal Structure of the PA5185 protein from Pseudomonas Aeruginosa Strain PAO1.

Components

Thioesterase

Keywords

HYDROLASE / thioesterase / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

fatty acyl-CoA hydrolase activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Chruszcz, M. / Wang, S. / Cymborowski, M. / Kudritska, M. / Evdokimova, E. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Cryst.Growth Des. / Year: 2008
Title: Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.
Authors: Chruszcz, M. / Zimmerman, M.D. / Wang, S. / Koclega, K.D. / Zheng, H. / Evdokimova, E. / Kudritska, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Minor, W.

History

Deposition	Aug 29, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 18, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.3	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Oct 30, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2av9.cif.gz	319.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2av9.ent.gz	259.2 KB	Display	PDB format
PDBx/mmJSON format	2av9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/2av9 ftp://data.pdbj.org/pub/pdb/validation_reports/av/2av9	HTTPS FTP

-
Related structure data

Related structure data	2o5uC 2o6bC 2o6tC 2o6uC C: citing same article (ref.)
Similar structure data	2o6b-1 2o6t-2 2o6u-1 2o6t-3 2o6t-1 2o5u-2 1bpy-d 5vpj-3 4ikv-d 3tm6-1 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
Other databases	TargetDB: APC5057

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Thioesterase

B: Thioesterase

C: Thioesterase

D: Thioesterase

E: Thioesterase

F: Thioesterase

G: Thioesterase

H: Thioesterase

I: Thioesterase

J: Thioesterase

K: Thioesterase

L: Thioesterase

hetero molecules

200 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thioesterase

B: Thioesterase

D: Thioesterase

E: Thioesterase

hetero molecules

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

2

C: Thioesterase

H: Thioesterase

I: Thioesterase

K: Thioesterase

hetero molecules

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

3

F: Thioesterase

G: Thioesterase

J: Thioesterase

L: Thioesterase

hetero molecules

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

Unit cell

Length a, b, c (Å)	241.661, 64.384, 117.469
Angle α, β, γ (deg.)	90.00, 105.40, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	GLU	GLU	2	A	A	8 - 50	8 - 50
2	1	1	LEU	LEU	GLU	GLU	2	G	G	8 - 50	8 - 50
3	1	1	LEU	LEU	GLU	GLU	2	H	H	8 - 50	8 - 50
4	1	1	LEU	LEU	GLU	GLU	2	I	I	8 - 50	8 - 50
5	1	1	LEU	LEU	GLU	GLU	2	L	L	8 - 50	8 - 50
6	2	1	GLU	GLU	GLU	GLU	2	A	A	60 - 122	60 - 122
7	2	1	GLU	GLU	GLU	GLU	2	G	G	60 - 122	60 - 122
8	2	1	GLU	GLU	GLU	GLU	2	H	H	60 - 122	60 - 122
9	2	1	GLU	GLU	GLU	GLU	2	I	I	60 - 122	60 - 122
10	2	1	GLU	GLU	GLU	GLU	2	L	L	60 - 122	60 - 122
11	3	1	ARG	ARG	GLN	GLN	2	A	A	127 - 143	127 - 143
12	3	1	ARG	ARG	GLN	GLN	2	G	G	127 - 143	127 - 143
13	3	1	ARG	ARG	GLN	GLN	2	H	H	127 - 143	127 - 143
14	3	1	ARG	ARG	GLN	GLN	2	I	I	127 - 143	127 - 143
15	3	1	ARG	ARG	GLN	GLN	2	L	L	127 - 143	127 - 143
1	1	2	LEU	LEU	GLU	GLU	2	A	A	8 - 50	8 - 50
2	1	2	LEU	LEU	GLU	GLU	2	E	E	8 - 50	8 - 50
3	1	2	LEU	LEU	GLU	GLU	2	F	F	8 - 50	8 - 50
4	1	2	LEU	LEU	GLU	GLU	2	B	B	8 - 50	8 - 50
5	1	2	LEU	LEU	GLU	GLU	2	C	C	8 - 50	8 - 50
6	1	2	LEU	LEU	GLU	GLU	2	D	D	8 - 50	8 - 50
7	1	2	LEU	LEU	GLU	GLU	2	J	J	8 - 50	8 - 50
8	1	2	LEU	LEU	GLU	GLU	2	K	K	8 - 50	8 - 50
9	2	2	GLU	GLU	LEU	LEU	2	A	A	60 - 104	60 - 104
10	2	2	GLU	GLU	LEU	LEU	2	E	E	60 - 104	60 - 104
11	2	2	GLU	GLU	LEU	LEU	2	F	F	60 - 104	60 - 104
12	2	2	GLU	GLU	LEU	LEU	2	B	B	60 - 104	60 - 104
13	2	2	GLU	GLU	LEU	LEU	2	C	C	60 - 104	60 - 104
14	2	2	GLU	GLU	LEU	LEU	2	D	D	60 - 104	60 - 104
15	2	2	GLU	GLU	LEU	LEU	2	J	J	60 - 104	60 - 104
16	2	2	GLU	GLU	LEU	LEU	2	K	K	60 - 104	60 - 104
17	3	2	GLU	GLU	GLU	GLU	2	A	A	109 - 122	109 - 122
18	3	2	GLU	GLU	GLU	GLU	2	E	E	109 - 122	109 - 122
19	3	2	GLU	GLU	GLU	GLU	2	F	F	109 - 122	109 - 122
20	3	2	GLU	GLU	GLU	GLU	2	B	B	109 - 122	109 - 122
21	3	2	GLU	GLU	GLU	GLU	2	C	C	109 - 122	109 - 122
22	3	2	GLU	GLU	GLU	GLU	2	D	D	109 - 122	109 - 122
23	3	2	GLU	GLU	GLU	GLU	2	J	J	109 - 122	109 - 122
24	3	2	GLU	GLU	GLU	GLU	2	K	K	109 - 122	109 - 122
25	4	2	ARG	ARG	GLN	GLN	2	A	A	127 - 143	127 - 143
26	4	2	ARG	ARG	GLN	GLN	2	E	E	127 - 143	127 - 143
27	4	2	ARG	ARG	GLN	GLN	2	F	F	127 - 143	127 - 143
28	4	2	ARG	ARG	GLN	GLN	2	B	B	127 - 143	127 - 143
29	4	2	ARG	ARG	GLN	GLN	2	C	C	127 - 143	127 - 143
30	4	2	ARG	ARG	GLN	GLN	2	D	D	127 - 143	127 - 143
31	4	2	ARG	ARG	GLN	GLN	2	J	J	127 - 143	127 - 143
32	4	2	ARG	ARG	GLN	GLN	2	K	K	127 - 143	127 - 143
1	1	3	GLU	GLU	GLU	GLU	1	E	E	50 - 60	50 - 60
2	1	3	GLU	GLU	GLU	GLU	1	F	F	50 - 60	50 - 60
3	1	3	GLU	GLU	GLU	GLU	1	B	B	50 - 60	50 - 60
1	1	4	GLU	GLU	GLU	GLU	1	A	A	50 - 60	50 - 60
2	1	4	GLU	GLU	GLU	GLU	1	I	I	50 - 60	50 - 60
3	1	4	GLU	GLU	GLU	GLU	1	J	J	50 - 60	50 - 60
4	1	4	GLU	GLU	GLU	GLU	1	K	K	50 - 60	50 - 60
5	1	4	GLU	GLU	GLU	GLU	1	L	L	50 - 60	50 - 60
6	1	4	GLU	GLU	GLU	GLU	1	C	C	50 - 60	50 - 60
7	1	4	GLU	GLU	GLU	GLU	1	D	D	50 - 60	50 - 60
8	1	4	GLU	GLU	GLU	GLU	1	G	G	50 - 60	50 - 60
9	1	4	GLU	GLU	GLU	GLU	1	H	H	50 - 60	50 - 60

NCS ensembles :

ID
1
2
3
4

Details

The most probable biological assembly is a tetramer. Chains C,H, I and K create the tetramer.

#1: Protein	Thioesterase Mass: 16527.473 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q9HU04
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Ammonium Sulphate, 0.1M Bis-Tris pH 5.5, 23% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97943, 0.97929, 0.96420

Detector

Type: SBC-3 / Detector: CCD / Date: May 5, 2004 / Details: mirror

Radiation

Monochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97943	1
2	0.97929	1
3	0.9642	1

Reflection

Resolution: 2.4→36.94 Å / Num. all: 68671 / Num. obs: 68671 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / R_merge(I) obs: 0.066 / Net I/σ(I): 12.5

Reflection shell

Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.348 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
HKL-2000		data scaling
HKL-3000		phasing
SHELXD		phasing
MLPHARE		phasing
DM		phasing
RESOLVE		phasing
SHARP		phasing
ARP/wARP		model building
CCP4		phasing
SHELXE		model building
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.4→36.94 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.91 / SU B: 18.763 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25334	3473	5.1 %	RANDOM
R_work	0.20402	-	-	-
obs	0.20653	65081	99.96 %	-
all	-	65081	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 42.481 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	0.2 Å²
2-	-	-0.1 Å²	0 Å²
3-	-	-	0.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→36.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12500	0	75	59	12634

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	12897
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.904	1.939	17611
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.622	5	1658
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.869	23.108	576
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.686	15	1726
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.327	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	1956
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10080
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	5453
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.319	0.2	8949
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	449
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	0.227	0.2	181
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.177	0.2	26
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	0.992	1.5	8411
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.685	2	13138
X-RAY DIFFRACTION	r_scbond_it	3.408	3	5057
X-RAY DIFFRACTION	r_scangle_it	4.835	4.5	4472
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	491	tight positional	0.1	0.05
1	2	G	491	tight positional	0.08	0.05
1	3	H	491	tight positional	0.09	0.05
1	4	I	491	tight positional	0.09	0.05
1	5	L	491	tight positional	0.08	0.05
2	1	A	471	tight positional	0.15	0.05
2	2	E	471	tight positional	0.14	0.05
2	3	F	471	tight positional	0.13	0.05
2	4	B	471	tight positional	0.19	0.05
2	5	C	471	tight positional	0.13	0.05
2	6	D	471	tight positional	0.14	0.05
2	7	J	471	tight positional	0.17	0.05
2	8	K	471	tight positional	0.11	0.05
3	1	E	59	tight positional	0.08	0.05
3	2	F	59	tight positional	0.09	0.05
3	3	B	59	tight positional	0.13	0.05
4	1	A	54	tight positional	0.07	0.05
4	2	I	54	tight positional	0.07	0.05
4	3	J	54	tight positional	0.08	0.05
4	4	K	54	tight positional	0.08	0.05
4	5	L	54	tight positional	0.08	0.05
4	6	C	54	tight positional	0.08	0.05
4	7	D	54	tight positional	0.07	0.05
4	8	G	54	tight positional	0.07	0.05
4	9	H	54	tight positional	0.06	0.05
1	1	A	387	medium positional	0.4	0.5
1	2	G	387	medium positional	0.39	0.5
1	3	H	387	medium positional	0.39	0.5
1	4	I	387	medium positional	0.37	0.5
1	5	L	387	medium positional	0.31	0.5
2	1	A	375	medium positional	0.56	0.5
2	2	E	375	medium positional	0.61	0.5
2	3	F	375	medium positional	0.59	0.5
2	4	B	375	medium positional	0.66	0.5
2	5	C	375	medium positional	0.56	0.5
2	6	D	375	medium positional	0.59	0.5
2	7	J	375	medium positional	0.67	0.5
2	8	K	375	medium positional	0.61	0.5
1	1	A	491	tight thermal	0.37	0.5
1	2	G	491	tight thermal	0.22	0.5
1	3	H	491	tight thermal	0.26	0.5
1	4	I	491	tight thermal	0.24	0.5
1	5	L	491	tight thermal	0.23	0.5
2	1	A	471	tight thermal	0.4	0.5
2	2	E	471	tight thermal	0.36	0.5
2	3	F	471	tight thermal	0.29	0.5
2	4	B	471	tight thermal	0.38	0.5
2	5	C	471	tight thermal	0.3	0.5
2	6	D	471	tight thermal	0.32	0.5
2	7	J	471	tight thermal	0.34	0.5
2	8	K	471	tight thermal	0.26	0.5
3	1	E	59	tight thermal	0.29	0.5
3	2	F	59	tight thermal	0.22	0.5
3	3	B	59	tight thermal	0.38	0.5
4	1	A	54	tight thermal	0.54	0.5
4	2	I	54	tight thermal	0.26	0.5
4	3	J	54	tight thermal	0.36	0.5
4	4	K	54	tight thermal	0.2	0.5
4	5	L	54	tight thermal	0.17	0.5
4	6	C	54	tight thermal	0.26	0.5
4	7	D	54	tight thermal	0.29	0.5
4	8	G	54	tight thermal	0.13	0.5
4	9	H	54	tight thermal	0.13	0.5
1	1	A	387	medium thermal	1.8	2
1	2	G	387	medium thermal	1.36	2
1	3	H	387	medium thermal	1.46	2
1	4	I	387	medium thermal	1.47	2
1	5	L	387	medium thermal	1.43	2
2	1	A	375	medium thermal	2.16	2
2	2	E	375	medium thermal	2.01	2
2	3	F	375	medium thermal	1.75	2
2	4	B	375	medium thermal	2.28	2
2	5	C	375	medium thermal	1.79	2
2	6	D	375	medium thermal	2.2	2
2	7	J	375	medium thermal	2.07	2
2	8	K	375	medium thermal	1.53	2

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	266	-
R_work	0.237	4741	-
obs	-	-	99.76 %

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	1.8895	-0.0725	-0.1005	2.4919	0.3564	1.1103	0.0051	0.1959	-0.1713	-0.1373	0.0207	-0.1239	-0.0842	0.073	-0.0258	-0.1248	0.0145	0.0115	-0.2728	0.0076	-0.354	44.674	46.15	67.755
2	1.6658	0.4146	-0.8191	1.3781	-0.6522	2.1536	0.0013	-0.2878	-0.4058	0.0483	-0.1878	-0.285	-0.0331	0.3843	0.1866	-0.1311	-0.0524	-0.0216	-0.1855	0.0452	-0.2348	67.163	10.96	45.338
3	2.4428	1.58	0.4408	1.5183	0.2204	2.2416	0.0729	0.2245	-0.4332	-0.1249	0.2246	-0.2683	0.1232	0.0133	-0.2974	-0.1067	0.029	-0.054	-0.1935	0.0494	0.1709	69.337	37.347	67.769
4	2.4241	-0.3423	0.2087	2.6335	0.0979	2.3746	-0.1138	-0.5271	-0.9112	0.1715	0.1428	0.0464	0.4335	0.173	-0.029	-0.0378	0.1045	0.0314	-0.1575	0.2314	0.0004	44.327	27.772	87.269
5	3.5077	-0.306	-0.7954	1.4682	0.4442	2.5125	-0.2772	-0.82	-0.5325	0.2899	0.1542	0.2934	0.1167	0.1531	0.123	-0.0753	0.0961	0.0708	-0.0504	0.2332	-0.1902	26.655	38.789	94.646
6	3.85	-0.4066	-0.5656	1.3841	-0.0974	2.8688	-0.2053	0.1869	-0.8141	0.0015	-0.2621	0.3591	0.2113	-0.3389	0.4675	-0.1466	-0.0426	0.0612	-0.0837	-0.0885	-0.0071	121.085	9.027	86.858
7	4.0946	0.3994	-2.1	1.8147	-0.1891	3.7054	-0.14	-0.1105	-0.534	0.2329	-0.2279	0.4581	-0.0064	-0.9106	0.3679	-0.1138	-0.0002	0.0455	0.3543	-0.1548	0.0027	103.113	17.556	96.552
8	3.7983	0.4321	1.1494	1.3373	-0.1924	3.2431	0.1228	-0.6468	-0.285	0.3061	0.1206	-0.1364	0.2593	0.1097	-0.2434	0.0513	0.1059	-0.0932	0.0826	-0.0061	0.0289	88.045	46.959	92.68
9	3.017	2.2246	0.8971	5.2283	1.5891	2.2362	0.0067	-0.5157	0.3021	0.062	0.0294	0.2858	-0.151	-0.1609	-0.0362	-0.104	0.0848	-0.0484	-0.0708	-0.0324	0.0911	69.668	57.168	85.852
10	2.4933	0.2711	-1.1528	1.7769	0.7079	2.5501	0.1208	-0.5738	0.1213	0.2147	-0.1326	-0.0271	-0.1413	0.064	0.0118	-0.0367	-0.0209	-0.0214	-0.0403	-0.0514	-0.2692	132.151	31.598	97.334
11	4.0165	0.9197	0.4954	0.7425	-0.6141	3.0845	0.1898	0.6174	-0.784	0.016	0.2039	0.0386	0.1027	0.8616	-0.3937	-0.0373	0.1184	-0.0694	0.1548	-0.223	0.1454	90.951	41.179	66.935
12	1.7868	-0.2961	-0.7025	1.5684	1.3139	3.4482	0.1465	-0.0676	0.4086	-0.0436	-0.053	-0.2647	-0.6119	0.631	-0.0935	0.1192	-0.2067	-0.0286	0.1146	0.1063	-0.0848	96.807	40.42	23.251

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	5 - 146	5 - 146
2	X-RAY DIFFRACTION	2	B	B	6 - 144	6 - 144
3	X-RAY DIFFRACTION	3	C	C	6 - 144	6 - 144
4	X-RAY DIFFRACTION	4	D	D	3 - 143	3 - 143
5	X-RAY DIFFRACTION	5	E	E	7 - 143	7 - 143
6	X-RAY DIFFRACTION	6	F	F	6 - 144	6 - 144
7	X-RAY DIFFRACTION	7	G	G	8 - 143	8 - 143
8	X-RAY DIFFRACTION	8	H	H	5 - 143	5 - 143
9	X-RAY DIFFRACTION	9	I	I	6 - 144	6 - 144
10	X-RAY DIFFRACTION	10	J	J	6 - 143	6 - 143
11	X-RAY DIFFRACTION	11	K	K	7 - 143	7 - 143
12	X-RAY DIFFRACTION	12	L	L	7 - 143	7 - 143

-
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