PDB-4j5i: Crystal structure of an alpha-ketoglutarate-dependent taurine dio...

ID or keywords:

Entry

Database: PDB / ID: 4j5i

Title

Crystal structure of an alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium smegmatis

Components

Alpha-ketoglutarate-dependent taurine dioxygenase

Keywords

OXIDOREDUCTASE /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID /

TauD / iron-dependent /

molecular oxygen

Function / homology

Function and homology information

taurine dioxygenase /

taurine dioxygenase activity /

metal ion binding
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...

History

Deposition	Feb 8, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2015	Group: Database references
Revision 1.2	Sep 20, 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_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 / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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	4j5i.cif.gz	777.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4j5i.ent.gz	644 KB	Display	PDB format
PDBx/mmJSON format	4j5i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j5/4j5i ftp://data.pdbj.org/pub/pdb/validation_reports/j5/4j5i	HTTPS FTP

-
Related structure data

Related structure data	3gvcC 3gvgC 3gwcC 3h7fC 3h81C 3he2C 3hwiC 3hwkC 3hzgC 3icoC 3khpC 3llsC 3moyC 3mpzC 3mybC 3ndnC 3ndoC 3nf4C 3ng3C 3njdC 3nwoC 3o0mC 3o38C 3oc6C 3oc7C 3oi9C 3oksC 3omeC 3p0tC 3p2yC 3p4iC 3p4tC 3p5mC 3p85C 3pe8C 3pk0C 3ppiC 3pzyC 3q1tC 3q8nC 3qbpC 3qdfC 3qhaC 3qivC 3qk8C 3qkaC 3qljC 3qmjC 3qreC 3quaC 3quvC 3qxiC 3qxzC 3qyrC 3r0oC 3r1iC 3r1jSC 3r20C 3r2nC 3r4tC 3r6hC 3r6oC 3r7kC 3r8cC 3r9pC 3r9qC 3r9rC 3r9sC 3r9tC 3rd5C 3rd7C 3rd8C 3rfqC 3rihC 3rr2C 3rr6C 3rrpC 3rrvC 3rsiC 3rv2C 3s82C 3sbxC 3sf6C 3sllC 3svkC 3svtC 3swoC 3swtC 3swxC 3t3wC 3tavC 3tcrC 3tdeC 3tjrC 3tl3C 3tlfC 3trrC 3tx2C 3tzqC 3tzuC 3u0aC 3u0bC 3ucxC 3uveC 4di1C 4dieC 4dq8C 4dxlC 4ed4C 4egeC 4egfC 4emdC 4eo9C 4eyeC 4f3wC 4f47C 4ffcC 4gk6C 4hdtC 4hr3C 4i1yC 4ijnC 4iv6C 4iz9C 4kamC 4lgvC 4o2dC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6pzh-d 3swt-3 6j33-2 3a6o-d 7kax-1 5zqk-1 1wzl-d 1x6m-d 1jib-d 6kr2-2 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
Other databases	TargetTrack: MysmA.01188.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alpha-ketoglutarate-dependent taurine dioxygenase

B: Alpha-ketoglutarate-dependent taurine dioxygenase

C: Alpha-ketoglutarate-dependent taurine dioxygenase

D: Alpha-ketoglutarate-dependent taurine dioxygenase

E: Alpha-ketoglutarate-dependent taurine dioxygenase

F: Alpha-ketoglutarate-dependent taurine dioxygenase

G: Alpha-ketoglutarate-dependent taurine dioxygenase

H: Alpha-ketoglutarate-dependent taurine dioxygenase

hetero molecules

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

1

A: Alpha-ketoglutarate-dependent taurine dioxygenase

B: Alpha-ketoglutarate-dependent taurine dioxygenase

C: Alpha-ketoglutarate-dependent taurine dioxygenase

D: Alpha-ketoglutarate-dependent taurine dioxygenase

hetero molecules

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

2

E: Alpha-ketoglutarate-dependent taurine dioxygenase

F: Alpha-ketoglutarate-dependent taurine dioxygenase

G: Alpha-ketoglutarate-dependent taurine dioxygenase

H: Alpha-ketoglutarate-dependent taurine dioxygenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.010, 166.680, 99.720
Angle α, β, γ (deg.)	90.000, 90.570, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	VAL	VAL	A	A	3 - 292	7 - 296
2	1	GLN	GLN	VAL	VAL	B	B	3 - 292	7 - 296
1	2	GLN	GLN	VAL	VAL	A	A	3 - 292	7 - 296
2	2	GLN	GLN	VAL	VAL	C	C	3 - 292	7 - 296
1	3	GLN	GLN	ALA	ALA	A	A	3 - 283	7 - 287
2	3	GLN	GLN	ALA	ALA	D	D	3 - 283	7 - 287
1	4	GLN	GLN	PRO	PRO	A	A	3 - 291	7 - 295
2	4	GLN	GLN	PRO	PRO	E	E	3 - 291	7 - 295
1	5	GLN	GLN	PRO	PRO	A	A	3 - 291	7 - 295
2	5	GLN	GLN	PRO	PRO	F	F	3 - 291	7 - 295
1	6	GLN	GLN	VAL	VAL	A	A	3 - 292	7 - 296
2	6	GLN	GLN	VAL	VAL	G	G	3 - 292	7 - 296
1	7	GLN	GLN	PRO	PRO	A	A	3 - 291	7 - 295
2	7	GLN	GLN	PRO	PRO	H	H	3 - 291	7 - 295
1	8	VAL	VAL	ASP	ASP	B	B	2 - 293	6 - 297
2	8	VAL	VAL	ASP	ASP	C	C	2 - 293	6 - 297
1	9	GLN	GLN	GLY	GLY	B	B	3 - 284	7 - 288
2	9	GLN	GLN	GLY	GLY	D	D	3 - 284	7 - 288
1	10	VAL	VAL	ASP	ASP	B	B	2 - 293	6 - 297
2	10	VAL	VAL	ASP	ASP	E	E	2 - 293	6 - 297
1	11	GLN	GLN	ASP	ASP	B	B	3 - 293	7 - 297
2	11	GLN	GLN	ASP	ASP	F	F	3 - 293	7 - 297
1	12	GLN	GLN	VAL	VAL	B	B	3 - 292	7 - 296
2	12	GLN	GLN	VAL	VAL	G	G	3 - 292	7 - 296
1	13	VAL	VAL	ASP	ASP	B	B	2 - 293	6 - 297
2	13	VAL	VAL	ASP	ASP	H	H	2 - 293	6 - 297
1	14	GLN	GLN	GLY	GLY	C	C	3 - 284	7 - 288
2	14	GLN	GLN	GLY	GLY	D	D	3 - 284	7 - 288
1	15	VAL	VAL	ASP	ASP	C	C	2 - 293	6 - 297
2	15	VAL	VAL	ASP	ASP	E	E	2 - 293	6 - 297
1	16	GLN	GLN	ASP	ASP	C	C	3 - 293	7 - 297
2	16	GLN	GLN	ASP	ASP	F	F	3 - 293	7 - 297
1	17	GLN	GLN	VAL	VAL	C	C	3 - 292	7 - 296
2	17	GLN	GLN	VAL	VAL	G	G	3 - 292	7 - 296
1	18	VAL	VAL	ASP	ASP	C	C	2 - 293	6 - 297
2	18	VAL	VAL	ASP	ASP	H	H	2 - 293	6 - 297
1	19	GLN	GLN	ALA	ALA	D	D	3 - 283	7 - 287
2	19	GLN	GLN	ALA	ALA	E	E	3 - 283	7 - 287
1	20	GLN	GLN	ALA	ALA	D	D	3 - 283	7 - 287
2	20	GLN	GLN	ALA	ALA	F	F	3 - 283	7 - 287
1	21	GLN	GLN	GLY	GLY	D	D	3 - 284	7 - 288
2	21	GLN	GLN	GLY	GLY	G	G	3 - 284	7 - 288
1	22	GLN	GLN	ALA	ALA	D	D	3 - 283	7 - 287
2	22	GLN	GLN	ALA	ALA	H	H	3 - 283	7 - 287
1	23	GLN	GLN	VAL	VAL	E	E	3 - 292	7 - 296
2	23	GLN	GLN	VAL	VAL	F	F	3 - 292	7 - 296
1	24	GLN	GLN	VAL	VAL	E	E	3 - 292	7 - 296
2	24	GLN	GLN	VAL	VAL	G	G	3 - 292	7 - 296
1	25	VAL	VAL	ASP	ASP	E	E	2 - 293	6 - 297
2	25	VAL	VAL	ASP	ASP	H	H	2 - 293	6 - 297
1	26	GLN	GLN	VAL	VAL	F	F	3 - 292	7 - 296
2	26	GLN	GLN	VAL	VAL	G	G	3 - 292	7 - 296
1	27	GLN	GLN	VAL	VAL	F	F	3 - 292	7 - 296
2	27	GLN	GLN	VAL	VAL	H	H	3 - 292	7 - 296
1	28	GLN	GLN	VAL	VAL	G	G	3 - 292	7 - 296
2	28	GLN	GLN	VAL	VAL	H	H	3 - 292	7 - 296

NCS ensembles :

#1: Protein	Alpha-ketoglutarate-dependent taurine dioxygenase Mass: 33543.336 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / Gene: MSMEG_3870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QZ23, taurine dioxygenase
#2: Chemical	ChemComp-FE / FE (III) ION / Iron Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.38 Å³/Da / Density % sol: 48.42 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MysmA.01188.a.A1 PS00650 at 20 mg/mL against Morpheus condition A2, 10% PEG 8000, 20% ethylene glycol, 30 mM MgCl, 30 mM CaCl2, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 233128a2, ...Details: MysmA.01188.a.A1 PS00650 at 20 mg/mL against Morpheus condition A2, 10% PEG 8000, 20% ethylene glycol, 30 mM MgCl, 30 mM CaCl2, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 233128a2, unique puck ID oqa0-7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48.42 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MysmA.01188.a.A1 PS00650 at 20 mg/mL against Morpheus condition A2, 10% PEG 8000, 20% ethylene glycol, 30 mM MgCl, 30 mM CaCl2, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 233128a2, ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 8, 2012 / Details: VariMax

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. all: 77167 / Num. obs: 76380 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / B_iso Wilson estimate: 30.271 Å² / R_merge(I) obs: 0.113 / Net I/σ(I): 10.33

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.6-2.67	0.393	3.68	20566	5648	1	99.1
2.67-2.74	0.36	4.02	20265	5516	1	99.1
2.74-2.82	0.289	4.87	19704	5342	1	99.6
2.82-2.91	0.269	5.15	19346	5227	1	99.5
2.91-3	0.22	5.99	18674	5045	1	99.5
3-3.11	0.189	6.98	17920	4900	1	99.3
3.11-3.22	0.159	8.08	17308	4737	1	99.3
3.22-3.36	0.134	9.35	16484	4510	1	99.4
3.36-3.51	0.116	10.81	15286	4324	1	98.8
3.51-3.68	0.097	12.8	14568	4166	1	99
3.68-3.88	0.086	14.14	13521	3937	1	98.9
3.88-4.11	0.076	14.9	12362	3700	1	98.5
4.11-4.39	0.061	18.01	11316	3488	1	98.3
4.39-4.75	0.058	18.63	10648	3270	1	98.4
4.75-5.2	0.066	16.71	10144	2993	1	98.5
5.2-5.81	0.081	13.94	9657	2726	1	99.5
5.81-6.71	0.079	14.46	8569	2423	1	99.2
6.71-8.22	0.065	16.58	6955	2019	1	98.5
8.22-11.63	0.045	22.82	5123	1574	1	97.3
11.63-50	0.04	25.61	2665	835	1	93

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	49.35 Å
Translation	3 Å	49.35 Å

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
StructureStudio		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3R1J

3r1j

Resolution: 2.6→49.4 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.889 / WR_factor R_free: 0.2086 / WR_factor R_work: 0.1887 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8605 / SU B: 19.33 / SU ML: 0.212 / SU R Cruickshank DPI: 0.8414 / SU R_free: 0.2953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.841 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2345	3833	5 %	RANDOM
R_work	0.211	-	-	-
obs	0.2122	76379	98.98 %	-

Solvent computation

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

Displacement parameters

B_iso max: 83.78 Å² / B_iso mean: 26.9535 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.52 Å²	-0 Å²	0.52 Å²
2-	-	-1.83 Å²	-0 Å²
3-	-	-	0.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→49.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15795	0	13	509	16317

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	16188
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	15010
X-RAY DIFFRACTION	r_angle_refined_deg	1.251	1.937	22153
X-RAY DIFFRACTION	r_angle_other_deg	1.095	3	34218
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.06	5	2036
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.11	22.912	735
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.654	15	2314
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.366	15	130
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	2551
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	18546
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	3878
X-RAY DIFFRACTION	r_mcbond_it	0.971	1.902	8204
X-RAY DIFFRACTION	r_mcbond_other	0.971	1.902	8203
X-RAY DIFFRACTION	r_mcangle_it	1.643	2.842	10217

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	14527	0.06
1	2	B	14527	0.06
2	1	A	14770	0.05
2	2	C	14770	0.05
3	1	A	14197	0.06
3	2	D	14197	0.06
4	1	A	14716	0.06
4	2	E	14716	0.06
5	1	A	14619	0.06
5	2	F	14619	0.06
6	1	A	14928	0.05
6	2	G	14928	0.05
7	1	A	14472	0.06
7	2	H	14472	0.06
8	1	B	15897	0.06
8	2	C	15897	0.06
9	1	B	14193	0.05
9	2	D	14193	0.05
10	1	B	14583	0.06
10	2	E	14583	0.06
11	1	B	14573	0.06
11	2	F	14573	0.06
12	1	B	15667	0.06
12	2	G	15667	0.06
13	1	B	14639	0.06
13	2	H	14639	0.06
14	1	C	14112	0.06
14	2	D	14112	0.06
15	1	C	14881	0.05
15	2	E	14881	0.05
16	1	C	14503	0.07
16	2	F	14503	0.07
17	1	C	15767	0.06
17	2	G	15767	0.06
18	1	C	14565	0.06
18	2	H	14565	0.06
19	1	D	14146	0.06
19	2	E	14146	0.06
20	1	D	14512	0.05
20	2	F	14512	0.05
21	1	D	14201	0.06
21	2	G	14201	0.06
22	1	D	14263	0.06
22	2	H	14263	0.06
23	1	E	14640	0.06
23	2	F	14640	0.06
24	1	E	14849	0.06
24	2	G	14849	0.06
25	1	E	14688	0.06
25	2	H	14688	0.06
26	1	F	14550	0.06
26	2	G	14550	0.06
27	1	F	14746	0.06
27	2	H	14746	0.06
28	1	G	14518	0.06
28	2	H	14518	0.06

LS refinement shell

Resolution: 2.6→2.667 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	245	-
R_work	0.293	5391	-
all	-	5636	-
obs	-	-	99.07 %

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	0.3499	0.5321	-0.0248	1.811	0.2757	0.2469	0.0539	-0.0027	0.0647	0.0968	-0.0398	0.1822	0.0317	0.0162	-0.0141	0.0934	-0.0173	0.0285	0.0272	-0.0074	0.0411	104.7263	44.3753	113.9221
2	0.3232	-0.1923	0.0638	1.1597	-0.0815	0.2307	0.0207	0.0125	-0.0122	-0.1095	-0.0338	0.0374	-0.0042	0.0084	0.0131	0.0677	0.0028	-0.0147	0.052	0.0124	0.0318	101.2046	2.5723	87.8578
3	0.0908	0.2786	0.0926	1.7281	0.0404	0.1637	-0.0031	-0.0087	-0.0545	-0.0606	0.0065	-0.3514	-0.0014	-0.0123	-0.0034	0.013	-0.0066	0.0326	0.0593	-0.009	0.1231	132.8106	38.1123	97.6397
4	0.5556	0.6767	0.0038	1.4853	0.0714	0.349	-0.0482	-0.0727	-0.0412	0.2058	0.007	-0.1076	0.0183	0.0802	0.0413	0.11	0.0415	-0.0209	0.0692	0.0169	0.0179	115.3444	-3.9384	116.3858
5	0.2111	-0.1689	-0.0274	1.8967	-0.1887	0.2591	0.0629	0.0344	-0.0169	0.1668	-0.109	-0.1699	-0.046	0.0399	0.0461	0.0642	-0.019	-0.0556	0.0448	0.0316	0.0619	163.3507	33.7767	163.857
6	0.4992	0.1549	-0.0695	1.2783	0.2023	0.3497	-0.0401	0.0499	-0.0128	0.1406	0.0145	0.0354	0.015	-0.0047	0.0256	0.0497	0.0119	0.0242	0.0641	-0.0149	0.0301	138.8752	-7.9441	160.2255
7	0.1851	0.1488	-0.2167	2.0395	0.3092	0.4105	0.0089	0.0314	0.0639	-0.1294	-0	0.3942	-0.0357	-0.0052	-0.0088	0.0201	0.0108	-0.0441	0.0541	0.0122	0.1546	134.6137	39.9533	148.5767
8	0.0841	0.061	-0.0658	1.746	0.2118	0.2501	-0.0198	0.0081	-0.0044	-0.2648	-0.014	-0.0799	-0.0166	0.0245	0.0338	0.107	-0.0172	0.0399	0.0786	-0.0093	0.0266	153.8379	-1.7927	131.5865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 292
2	X-RAY DIFFRACTION	1	A	401
3	X-RAY DIFFRACTION	2	B	2 - 293
4	X-RAY DIFFRACTION	2	B	401
5	X-RAY DIFFRACTION	3	C	2 - 293
6	X-RAY DIFFRACTION	3	C	401
7	X-RAY DIFFRACTION	4	D	3 - 284
8	X-RAY DIFFRACTION	4	D	401
9	X-RAY DIFFRACTION	5	E	2 - 293
10	X-RAY DIFFRACTION	5	E	401
11	X-RAY DIFFRACTION	6	F	3 - 295
12	X-RAY DIFFRACTION	6	F	401
13	X-RAY DIFFRACTION	7	G	3 - 292
14	X-RAY DIFFRACTION	7	G	401
15	X-RAY DIFFRACTION	8	H	2 - 293
16	X-RAY DIFFRACTION	8	H	401

-
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