PDB-8cje: AetF, a single-component flavin-dependent tryptophan halogenase, ...

ID or keywords:

Entry

Database: PDB / ID: 8cje

Title

AetF, a single-component flavin-dependent tryptophan halogenase, in complex with L-tryptophan

Components

AetF

Keywords

FLAVOPROTEIN / single-component flavin-dependent halogenase / Aetokthonotoxin / single-component monooxygenase / tryptophan halogenase

Function / homology

FAD/NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / FLAVIN-ADENINE DINUCLEOTIDE / TRYPTOPHAN / AetF

Function and homology information

Biological species

Aetokthonos hydrillicola Thurmond2011 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Gafe, S. / Niemann, H.H.

Funding support

Germany, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF.
Authors: Gafe, S. / Niemann, H.H.

History

Deposition	Feb 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 28, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jul 12, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8cje.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb8cje.ent.gz	869.6 KB	Display	PDB format
PDBx/mmJSON format	8cje.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8cje_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8cje_full_validation.pdf.gz	2.6 MB	Display
Data in XML	8cje_validation.xml.gz	98.8 KB	Display
Data in CIF	8cje_validation.cif.gz	141.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/8cje ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cje	HTTPS FTP

-
Related structure data

Related structure data	8cjdSC 8cjfC 8cjgC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15151/ESRF-DC-1089735712 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: AetF

B: AetF

C: AetF

D: AetF

hetero molecules

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

1

A: AetF

hetero molecules

defined by author
Evidence: gel filtration, elution volume corresponds to the monomeric protein
78.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AetF

hetero molecules

defined by author
Evidence: gel filtration, elution volume corresponds to the monomeric protein
78.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: AetF

hetero molecules

defined by author
Evidence: gel filtration, elution volume corresponds to the monomeric protein
78.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: AetF

hetero molecules

defined by author
Evidence: gel filtration, elution volume corresponds to the monomeric protein
78.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.265, 173.718, 173.961
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 1 through 248 or resid 250 through 607 or resid 632 through 702))
d_2	ens_1	(chain "B" and (resid 1 through 248 or resid 250 through 607 or resid 632 through 702))
d_3	ens_1	(chain "C" and (resid 1 through 248 or resid 250 through 607 or resid 632 through 702))
d_4	ens_1	(chain "D" and (resid 1 through 248 or resid 250 through 607 or resid 632 through 702))

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	MET	MET	SER	SER	A	A	1 - 248	9 - 256
d_1	2	PRO	PRO	SER	SER	A	A	250 - 607	258 - 615
d_1	3	ALA	ALA	SER	SER	A	A	632 - 655	640 - 663
d_1	4	FAD	FAD	FAD	FAD	A	E	701
d_1	5	TRP	TRP	TRP	TRP	A	F	702
d_2	1	MET	MET	SER	SER	B	B	1 - 248	9 - 256
d_2	2	PRO	PRO	SER	SER	B	B	250 - 607	258 - 615
d_2	3	ALA	ALA	SER	SER	B	B	632 - 655	640 - 663
d_2	4	FAD	FAD	FAD	FAD	B	G	701
d_2	5	TRP	TRP	TRP	TRP	B	H	702
d_3	1	MET	MET	SER	SER	C	C	1 - 248	9 - 256
d_3	2	PRO	PRO	SER	SER	C	C	250 - 607	258 - 615
d_3	3	ALA	ALA	SER	SER	C	C	632 - 655	640 - 663
d_3	4	FAD	FAD	FAD	FAD	C	I	701
d_3	5	TRP	TRP	TRP	TRP	C	J	702
d_4	1	MET	MET	SER	SER	D	D	1 - 248	9 - 256
d_4	2	PRO	PRO	SER	SER	D	D	250 - 607	258 - 615
d_4	3	ALA	ALA	SER	SER	D	D	632 - 655	640 - 663
d_4	4	FAD	FAD	FAD	FAD	D	K	701
d_4	5	TRP	TRP	TRP	TRP	D	L	702

#1: Protein	AetF Mass: 77098.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria) Gene: aetF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B9Z9
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1239 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.64 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Condition A6, Morpheus Green Screen (Molecular Dimensions), 30 mM CaCl2, 30 mM MgCl2, 0.1 M HEPES/MOPS pH 7.5, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 6 mg/mL AetF (50 mM HEPES pH 7. ...Details: Condition A6, Morpheus Green Screen (Molecular Dimensions), 30 mM CaCl2, 30 mM MgCl2, 0.1 M HEPES/MOPS pH 7.5, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 6 mg/mL AetF (50 mM HEPES pH 7.0, 100 mM NaCl, 1 mM DTT), drop with 300 nL protein + 300 nL reservoir, crystals soaked with 250 nL L-Trp solution (37.5 mM L-Trp, 25 % (v/v) ethylene glycol)

Crystal

Density Matthews: 2.14 Å³/Da / Density % sol: 42.64 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Condition A6, Morpheus Green Screen (Molecular Dimensions), 30 mM CaCl2, 30 mM MgCl2, 0.1 M HEPES/MOPS pH 7.5, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 6 mg/mL AetF (50 mM HEPES pH 7. ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 25, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection twin	Type: pseudo-merohedral / Operator: -h,-l,-k / Fraction: 0.45
Reflection	Resolution: 1.8→50 Å / Num. obs: 244069 / % possible obs: 99.9 % / Redundancy: 13.29 % / B_iso Wilson estimate: 34.7 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.193 / Net I/σ(I): 10.19
Reflection shell	Resolution: 1.8→1.91 Å / Redundancy: 13.62 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 38986 / CC_1/2: 0.251 / R_rim(I) all: 3.095 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
MxCuBE	MXCuBE3	data collection
XDS	BUILT=20220110	data reduction
XDS	BUILT=20220110	data scaling
PHASER	2.8.3	phasing
Coot	0.9.4.1 EL	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8CJD

8cjd

Resolution: 1.8→48.3 Å / Cross valid method: FREE R-VALUE / σ(F): 397.02 / Phase error: 19.3664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1884	12211	5.01 %
R_work	0.1603	231613	-
obs	0.1808	243824	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 30.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→48.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20949	0	272	1239	22460

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0088	21796
X-RAY DIFFRACTION	f_angle_d	0.9673	29568
X-RAY DIFFRACTION	f_chiral_restr	0.0589	3125
X-RAY DIFFRACTION	f_plane_restr	0.0075	3790
X-RAY DIFFRACTION	f_dihedral_angle_d	14.2913	7981

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.722228457718
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.788371629034
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.73991764238

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.83	0.4095	598	0.3889	11326	X-RAY DIFFRACTION	93.7
1.83-1.86	0.3502	601	0.3455	11441	X-RAY DIFFRACTION	94.73
1.86-1.9	0.3428	604	0.33	11473	X-RAY DIFFRACTION	94.94
1.9-1.94	0.3185	607	0.2953	11526	X-RAY DIFFRACTION	94.99
1.94-1.98	0.293	606	0.2735	11505	X-RAY DIFFRACTION	95
1.98-2.03	0.2917	606	0.2583	11524	X-RAY DIFFRACTION	95
2.03-2.08	0.2698	604	0.2394	11462	X-RAY DIFFRACTION	94.99
2.08-2.13	0.2534	606	0.2203	11521	X-RAY DIFFRACTION	95
2.13-2.2	0.2399	607	0.2136	11527	X-RAY DIFFRACTION	95
2.2-2.27	0.23	606	0.2024	11517	X-RAY DIFFRACTION	94.99
2.27-2.35	0.217	609	0.1928	11573	X-RAY DIFFRACTION	95
2.35-2.44	0.2221	607	0.1868	11539	X-RAY DIFFRACTION	95
2.44-2.55	0.2093	609	0.1794	11578	X-RAY DIFFRACTION	95
2.55-2.69	0.2013	608	0.1705	11544	X-RAY DIFFRACTION	95
2.69-2.86	0.1951	612	0.166	11632	X-RAY DIFFRACTION	95
2.86-3.08	0.2016	611	0.1689	11610	X-RAY DIFFRACTION	95
3.08-3.39	0.2078	614	0.172	11663	X-RAY DIFFRACTION	94.99
3.39-3.88	0.1957	616	0.1666	11710	X-RAY DIFFRACTION	95
3.88-4.88	0.1701	621	0.1417	11796	X-RAY DIFFRACTION	95
4.88-48.3	0.1709	641	0.1484	12164	X-RAY DIFFRACTION	94.93

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	1.26408113425	-0.54393228221	-0.623069343255	1.17112893764	0.287805406782	1.92427017952	-0.004667306762	0.0539408938781	0.129258360082	-0.0522187888895	-0.0351558302307	-0.0805251825111	-0.0897449839751	0.0786217309062	0.0361818888717	0.240161202675	-0.0272839766666	-0.0208504877135	0.19226456844	0.00194592803575	0.212255193251	57.416995351	-20.2567130183	-39.905611231
2	1.87790670608	0.626799790709	1.09083718034	0.54421150789	0.200499944528	4.02947591473	0.0125294832597	0.217617699416	0.0630002720927	-0.0596294628098	0.0562113968029	-0.125360601083	-0.132691252436	0.280421625755	-0.0734127679129	0.226270718215	0.0267700929084	0.0198025894919	0.201063589665	0.0128014885307	0.248314596265	57.7221768751	-19.0832850006	-51.1599887963
3	0.11291125867	-0.144566490204	-0.100838091277	0.251647540422	0.275168135355	0.390572631464	0.0981687487132	0.0751909633991	0.0933921443203	-0.19147752102	-0.101264487296	0.00516253153591	-0.248503016204	0.0120802080364	-0.00744534881369	0.351616649494	-0.00662969941058	-0.00373189550585	0.258267241206	0.0157504603235	0.249130786886	46.2303958258	-11.9346800252	-46.9228345533
4	0.42928842661	-0.151808899948	0.0643297195082	0.581028973177	0.0711179185886	0.32650636308	-0.0168273884276	0.00197036767954	0.00388026918011	0.0273801885946	0.00806002110467	0.00771119350179	0.0186641827443	-0.0424923152883	0.0091484578509	0.266050796255	0.00138190962913	0.00285971365978	0.211131841068	-0.00110367423541	0.177301631687	33.9647076809	-17.9968770021	-27.0112283282
5	0.710611377079	-0.0448719278041	0.256644270408	0.380051210602	-0.145579126417	1.05095193908	0.0067895292646	0.0617293657775	-0.0542471675737	-0.0548135614151	-0.0114179075304	0.0141886691783	0.144929245062	0.0474552955332	-0.0140089657997	0.314338552804	0.030887288675	-0.0148369025875	0.191632411949	-0.0193559006874	0.210382103098	49.5407555572	-36.2346205664	-40.7406081961
6	1.19220517137	0.010558995377	-0.157674203129	0.376076874997	-0.0694065925877	0.673391486079	-0.0480796053358	-0.0635876033967	0.00997221701826	0.104889904292	0.0825864515826	0.0962286847601	-0.0033550595475	-0.0611136797744	-0.0362125707356	0.262885486793	0.00278650620503	-0.00274368583353	0.192870308291	-0.0115496875337	0.127799754086	37.394030594	-19.7473675608	-15.8787081028
7	0.677809503531	-0.553336958435	-0.155758854483	0.971739665033	-0.0205937540327	0.522325059419	-0.10171540953	-0.167790153914	-0.162378478419	0.196606700506	0.0797850499503	0.10479799631	0.166634369342	0.0323187232391	0.0255096192624	0.322522744982	-0.023596499902	-0.0329981702413	0.258356579878	0.0107579273549	0.228532334457	38.07642068	-33.6664317082	-19.4305852735
8	1.19603364936	-0.313297501784	-0.106282409485	0.80247581136	-0.173074700643	2.15229351074	0.0209268680663	0.130628278331	-0.191272350908	-0.070241551541	-0.0177847164455	0.145988353262	0.0762048516963	-0.202439492057	0.000576374698686	0.227515067479	-0.0207314322107	-0.00417375597414	0.226249419403	-0.0255488473127	0.252309945472	-13.2673344369	-63.0499514248	-41.8271851985
9	0.0496641601964	-0.138375143769	0.0640208717176	0.562805107313	-0.44807753553	0.434595942297	0.105476729336	0.187306105806	-0.0933383389832	-0.252157467906	-0.177583526802	-0.0107427530397	0.236883427503	0.0634973781951	0.0575746969382	0.307962023921	0.00611097319256	-0.00235442626264	0.319672871636	-0.0191703034943	0.276353737498	-2.09083908791	-71.2434151916	-45.4247707343
10	0.499012052288	-0.134366730984	-0.00707464968547	0.860608327343	-0.0918945815939	0.293441106994	-0.0382823100838	0.0134262117182	-0.00614199305717	0.0633912339266	0.0372194544753	-0.0422293105944	-0.00390236703461	0.043221544192	0.00288466379434	0.225844651759	-0.00511408624414	-0.0147432605713	0.216479805687	-0.0261477667364	0.181718487464	10.6385586363	-66.1789335496	-25.3881323225
11	1.04811684145	-0.337065858808	-0.205988176552	0.756774352365	0.32111260003	1.06261747001	0.00781844553124	0.0273674096098	0.0481261954317	0.0248929817278	0.00744447149095	-0.044459113239	-0.104695134125	0.000762088265874	-0.0192362252759	0.261318641584	0.00934096997757	-0.0121367348891	0.203406104843	0.00516950291941	0.218550883649	-4.33299819642	-46.9551288551	-36.4429722938
12	0.521195484428	-0.381799579413	0.210910476458	1.21496462091	-0.00126463496758	0.692962235692	-0.0912726570804	-0.130337237201	0.0806640384766	0.268328106248	0.083283811359	-0.090269582628	-0.0609789312321	0.0117660498543	0.0110542371722	0.26971072663	-0.0082551164401	0.00241780159766	0.285482623715	-0.0165669770137	0.233474637941	7.86701705394	-58.0550995317	-16.1199755748
13	1.08370445445	-0.44206560213	0.3442495413	2.29590334786	-0.145985840406	0.829967227364	0.0290234396542	-0.233656853929	-0.186367286981	0.080841364364	0.0733171793961	0.210557096902	0.0868014885705	-0.161351005151	-0.0975341809855	0.233650159352	-0.0257979181236	-0.00356348135087	0.285293917445	0.0356511514825	0.232154699984	7.98356255803	-85.6847126093	-64.3648774787
14	0.354712791158	0.0292512907444	0.335148860839	0.465655435878	0.0753811879005	0.470358558762	-0.0134108842499	-0.0418358088723	-0.00971559947546	0.0347045311387	0.0136019797819	-0.0204612962142	-0.00698085074012	-0.0315843794579	-0.00106531986773	0.230790883963	-0.00685412975823	0.00621076137543	0.200266129358	-0.0101133967918	0.192092464077	30.8122429927	-69.8051550196	-61.3751788089
15	0.7548780293	-0.0715874204313	-0.0234570797554	4.08083855112	-2.17052854762	1.1681205421	0.0504571557348	-0.0932853207949	-0.199523524647	-0.413518973243	-0.0244079471567	-0.0237467771969	0.220329619076	0.0553553221552	-0.0483341455167	0.284647524957	0.00403581403386	-0.0347131240416	0.244461474776	6.23664109649E-5	0.274823775172	21.5345589455	-96.8581879109	-76.0854960952
16	0.784124085374	0.00772863263259	0.285033260534	0.676321247713	0.126263561819	0.488014254879	0.0176457715098	0.0485001903363	0.000975287269089	-0.109177912073	-0.015138560988	0.00423512781195	-0.00971324483962	-0.0105987100947	-7.35532726944E-5	0.283774270897	0.00242757513022	-0.00622244564681	0.212988605367	0.00809184816568	0.188509338072	18.2717169399	-72.1776882313	-80.881417238
17	2.62724918997	-0.742583942509	0.32349178138	0.738772589327	0.00914857286221	0.103082981482	-0.08508398623	-0.496458988291	0.171064396508	0.192595922918	0.0452640066108	-0.0825486335628	-0.133501515755	-0.0752734379485	0.0284714105282	0.353411103143	0.0146076079295	-0.0149845047787	0.326782141976	-0.0881608728611	0.288320257844	33.4609855856	-59.2238538583	-45.471677598
18	0.695859507629	0.0529209879234	0.685104195754	0.413799319157	-0.0418693469613	1.13379504925	-0.131137395139	0.116279492189	0.198508529331	-0.115285969175	0.042010626273	0.0454401620519	-0.221752129207	0.0736118803485	0.0879254344032	0.325296436245	0.016115582001	0.00532202941335	0.262263591	-0.00398898508223	0.261562211417	24.9964762587	-60.0208598729	-82.3137751071
19	1.31275409595	0.068575836832	-0.555447037244	2.40470086068	-0.41826573436	1.53884643602	-0.017260655325	-0.186689220604	0.126438583781	0.0665401117149	0.110058289475	-0.0849002693069	-0.0308265117053	0.0940561324127	-0.0952643230866	0.178325609277	0.0021294403188	-0.0284167225677	0.188840541923	-0.0209560496104	0.157223073981	35.0571106773	-3.18913694408	-66.5014473957
20	1.36349632076	-0.50803514162	0.5107252798	2.61033112374	0.0870146080324	0.433528959426	0.125897285278	-0.0209919595764	0.259967058151	0.170300645071	-0.112348263963	-0.180285481659	-0.130035494035	0.135997015775	-0.00713492914603	0.285346111105	-0.0298246277106	0.0611110150998	0.259385168092	-0.0318816741095	0.231212545519	35.4078756765	8.07035536225	-65.5001513464
21	0.331291195771	-0.00952066583143	-0.240618335226	0.430341697814	-0.0360638510119	0.376597297592	0.00309668391135	-0.00921693921439	0.0338904326999	0.023947050825	0.0222936225421	0.0107623209287	0.0102797661835	-0.0351907600881	-0.0257770962988	0.268747023403	-0.0096629558553	-0.0150122282034	0.230400727867	0.000454994652755	0.202852593178	13.5352631482	-12.8087515234	-62.616488561
22	1.12850935244	0.319580363699	0.0741566047192	2.54180995827	1.48462424143	0.890708355569	0.0955339039611	-0.0105437142164	0.231385288049	-0.262578665745	-0.0299904827504	0.108615945517	-0.128167693993	-0.0361650161044	-0.057628885218	0.301363387176	0.0199178255817	0.0205536120611	0.23751735144	0.0110053282646	0.222302335276	21.4605617292	9.21712856407	-76.4764355403
23	0.980258920203	-0.102348767092	0.123505549714	1.10155610084	-0.23200354459	0.321258806452	0.0145818900573	0.050447353279	0.0546604199108	-0.134569685492	-0.0185638818021	-0.041804544736	-0.0284005343537	-0.0188930246675	0.000288382144656	0.290534721571	-0.00251272783796	0.0211165100832	0.21020764848	0.0123556888621	0.178512838168	27.3507358217	-4.88639972755	-84.9066897229
24	0.631653486729	-0.0604806919507	-0.150471898203	0.344248505289	0.0727264478921	0.548250847207	-0.00331852844287	-0.000918083445454	-0.104071975544	0.00516192025098	-0.00955621361287	0.0217788450592	0.135076211212	-0.0918072524176	0.0275207014062	0.308262201466	-0.0181263100306	-0.00969158566947	0.187935948906	0.0133399861211	0.237817204988	14.5313063899	-28.1892291974	-67.3622931288
25	0.537697198453	0.122876303888	-0.0820900313533	2.06817513629	0.756298342338	1.38593028976	-0.0237703521535	0.109784594695	-0.0840704158439	-0.333063442215	0.0937034504808	-0.0437574259666	0.06459258932	-0.0135006890093	-0.047981593452	0.227697793677	0.00608915952852	0.00709103210547	0.248921724611	-0.00984452019778	0.182522532773	23.7512446248	-15.7971848308	-89.9259143214

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 75 )	A	A	1 - 75	1 - 75
2	2	chain 'A' and (resid 76 through 113 )	A	A	76 - 113	76 - 113
3	3	chain 'A' and (resid 114 through 148 )	A	A	114 - 148	114 - 148
4	4	chain 'A' and (resid 149 through 334 )	A	A	149 - 334	149 - 334
5	5	chain 'A' and (resid 335 through 491 )	A	A	335 - 491	335 - 491
6	6	chain 'A' and (resid 492 through 558 )	A	A	492 - 558	492 - 558
7	7	chain 'A' and (resid 559 through 702 )	A	A - C	559 - 702	559 - 634
8	8	chain 'B' and (resid 1 through 113 )	B	D	1 - 113	1 - 113
9	9	chain 'B' and (resid 114 through 148 )	B	D	114 - 148	114 - 148
10	10	chain 'B' and (resid 149 through 334 )	B	D	149 - 334	149 - 334
11	11	chain 'B' and (resid 335 through 504 )	B	D	335 - 504	335 - 504
12	12	chain 'B' and (resid 505 through 702 )	B	D - F	505 - 702	505 - 634
13	13	chain 'C' and (resid 1 through 121 )	C	G	1 - 121	1 - 121
14	14	chain 'C' and (resid 122 through 334 )	C	G	122 - 334	122 - 334
15	15	chain 'C' and (resid 335 through 365 )	C	G	335 - 365	335 - 365
16	16	chain 'C' and (resid 366 through 530 )	C	G	366 - 530	366 - 530
17	17	chain 'C' and (resid 531 through 568 )	C	G	531 - 568	531 - 568
18	18	chain 'C' and (resid 569 through 702 )	C	G - I	569 - 702	569 - 634
19	19	chain 'D' and (resid 1 through 75 )	D	J	1 - 75	1 - 75
20	20	chain 'D' and (resid 76 through 113 )	D	J	76 - 113	76 - 113
21	21	chain 'D' and (resid 114 through 334 )	D	J	114 - 334	114 - 334
22	22	chain 'D' and (resid 335 through 375 )	D	J	335 - 375	335 - 375
23	23	chain 'D' and (resid 376 through 479 )	D	J	376 - 479	376 - 479
24	24	chain 'D' and (resid 480 through 600 )	D	J	480 - 600	480 - 600
25	25	chain 'D' and (resid 601 through 702 )	D	J - L	601 - 702	601 - 634

-
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