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

ID or keywords:

Entry

Database: PDB / ID: 8cjf

Title

AetF, a single-component flavin-dependent tryptophan halogenase, in complex with 5-bromo-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 / 5-bromo-L-tryptophan / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / AetF

Function and homology information

Biological species

Aetokthonos hydrillicola Thurmond2011 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 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	8cjf.cif.gz	943.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8cjf.ent.gz	656.5 KB	Display	PDB format
PDBx/mmJSON format	8cjf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8cjf_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8cjf_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8cjf_validation.xml.gz	51.1 KB	Display
Data in CIF	8cjf_validation.cif.gz	73.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/8cjf ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cjf	HTTPS FTP

-
Related structure data

Related structure data	8cjdSC 8cjeC 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-1089719643 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AetF

B: AetF

hetero molecules

157 kDa, 2 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
78.4 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
78.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.700, 122.700, 87.418
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃
Space group name Hall	P4cw
Symmetry operation	#1: x,y,z #2: -y,x,z+3/4 #3: y,-x,z+1/4 #4: -x,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 1 through 17 or resid 19...
d_2	ens_1	(chain "B" and (resid 1 through 17 or resid 19...

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	VAL	VAL	A	A	1 - 17	9 - 25
d_1	2	GLU	GLU	PHE	PHE	A	A	19 - 55	27 - 63
d_1	3	THR	THR	ASP	ASP	A	A	57 - 197	65 - 205
d_1	4	LEU	LEU	SER	SER	A	A	199 - 248	207 - 256
d_1	5	PRO	PRO	ARG	ARG	A	A	250 - 318	258 - 326
d_1	6	PHE	PHE	TYR	TYR	A	A	320 - 346	328 - 354
d_1	7	TYR	TYR	THR	THR	A	A	348 - 369	356 - 377
d_1	8	PRO	PRO	ALA	ALA	A	A	371 - 495	379 - 503
d_1	9	VAL	VAL	SER	SER	A	A	497 - 655	505 - 663
d_1	10	FAD	FAD	FAD	FAD	A	C	701
d_1	11	64X	64X	64X	64X	A	D	702
d_1	12	PEG	PEG	PEG	PEG	A	E	703
d_1	13	PEG	PEG	PEG	PEG	A	F	704
d_2	1	MET	MET	VAL	VAL	B	B	1 - 17	9 - 25
d_2	2	GLU	GLU	PHE	PHE	B	B	19 - 55	27 - 63
d_2	3	THR	THR	ASP	ASP	B	B	57 - 197	65 - 205
d_2	4	LEU	LEU	SER	SER	B	B	199 - 248	207 - 256
d_2	5	PRO	PRO	ARG	ARG	B	B	250 - 318	258 - 326
d_2	6	PHE	PHE	TYR	TYR	B	B	320 - 346	328 - 354
d_2	7	TYR	TYR	THR	THR	B	B	348 - 369	356 - 377
d_2	8	PRO	PRO	ALA	ALA	B	B	371 - 495	379 - 503
d_2	9	VAL	VAL	LEU	LEU	B	B	497 - 609	505 - 617
d_2	10	CYS	CYS	SER	SER	B	B	628 - 655	636 - 663
d_2	11	FAD	FAD	FAD	FAD	B	H	701
d_2	12	64X	64X	64X	64X	B	I	702
d_2	13	PEG	PEG	PEG	PEG	B	J	703
d_2	14	PEG	PEG	PEG	PEG	B	K	704

NCS oper: (Code: givenMatrix: (-0.0439606717348, 0.998703812021, 0.0256545355659), (0.99898403924, 0.0436890986214, 0.0110522398507), (0.0099170905358, 0.0261143354525, -0.99960977026)Vector: 64. ...

-
Protein , 1 types, 2 molecules AB

#1: Protein	AetF Mass: 77098.727 Da / Num. of mol.: 2 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

-
Non-polymers , 5 types, 641 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-64X / 5-bromo-L-tryptophan Mass: 283.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₁BrN₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H₂O

-
Details

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: 42.54 %
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, 300 nL saturated 5-bromo-L-tryptophan dried up on plate prior to adding protein and reservoir

Crystal

Density Matthews: 2.14 Å³/Da / Density % sol: 42.54 %

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	Resolution: 1.9→50 Å / Num. obs: 201422 / % possible obs: 99.8 % / Redundancy: 6.91 % / B_iso Wilson estimate: 38.8 Å² / CC_1/2: 0.996 / R_rim(I) all: 0.193 / Net I/σ(I): 6.55
Reflection shell	Resolution: 1.9→2.01 Å / Redundancy: 7.07 % / Mean I/σ(I) obs: 0.43 / Num. unique obs: 32268 / CC_1/2: 0.191 / R_rim(I) all: 2.616 / % possible all: 98.8

-
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:

FOURIER SYNTHESIS
Starting model: 8CJD

8cjd

Resolution: 1.9→46.48 Å / SU ML: 0.2808 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2075	9993	5 %
R_work	0.1831	189995	-
obs	0.1843	199988	99.51 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.28 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→46.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10563	0	168	631	11362

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11130
X-RAY DIFFRACTION	f_angle_d	0.5785	15103
X-RAY DIFFRACTION	f_chiral_restr	0.0432	1588
X-RAY DIFFRACTION	f_plane_restr	0.0046	1944
X-RAY DIFFRACTION	f_dihedral_angle_d	13.8674	4093

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.589949660448 Å

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 (%)
1.9-1.92	0.3996	296	0.3774	5866	X-RAY DIFFRACTION	91.74
1.92-1.94	0.3847	320	0.3635	6169	X-RAY DIFFRACTION	96.2
1.94-1.97	0.3346	331	0.3485	6269	X-RAY DIFFRACTION	99.35
1.97-1.99	0.3445	334	0.332	6343	X-RAY DIFFRACTION	99.63
1.99-2.02	0.312	341	0.322	6457	X-RAY DIFFRACTION	99.88
2.02-2.05	0.3519	329	0.314	6267	X-RAY DIFFRACTION	99.86
2.05-2.08	0.3293	330	0.3016	6325	X-RAY DIFFRACTION	99.94
2.08-2.11	0.3277	336	0.2884	6391	X-RAY DIFFRACTION	99.97
2.11-2.14	0.3016	338	0.2827	6380	X-RAY DIFFRACTION	99.94
2.14-2.17	0.2778	328	0.2765	6279	X-RAY DIFFRACTION	99.92
2.18-2.21	0.2665	337	0.2637	6431	X-RAY DIFFRACTION	99.9
2.21-2.25	0.2877	335	0.2528	6355	X-RAY DIFFRACTION	99.94
2.25-2.3	0.2571	333	0.2406	6333	X-RAY DIFFRACTION	100
2.3-2.34	0.2621	335	0.2293	6355	X-RAY DIFFRACTION	99.96
2.34-2.39	0.2413	339	0.2227	6369	X-RAY DIFFRACTION	99.97
2.39-2.45	0.2385	337	0.2099	6352	X-RAY DIFFRACTION	100
2.45-2.51	0.2141	337	0.2007	6388	X-RAY DIFFRACTION	100
2.51-2.58	0.2486	334	0.2046	6343	X-RAY DIFFRACTION	99.99
2.58-2.65	0.2265	334	0.1959	6365	X-RAY DIFFRACTION	99.99
2.65-2.74	0.2235	337	0.1896	6410	X-RAY DIFFRACTION	100
2.74-2.84	0.2111	334	0.1828	6336	X-RAY DIFFRACTION	100
2.84-2.95	0.2291	337	0.1835	6364	X-RAY DIFFRACTION	100
2.95-3.09	0.2169	336	0.1869	6360	X-RAY DIFFRACTION	99.99
3.09-3.25	0.1903	336	0.1806	6335	X-RAY DIFFRACTION	99.99
3.25-3.45	0.2082	334	0.1703	6351	X-RAY DIFFRACTION	100
3.45-3.72	0.2097	340	0.1612	6371	X-RAY DIFFRACTION	99.97
3.72-4.09	0.1678	334	0.1338	6357	X-RAY DIFFRACTION	100
4.09-4.68	0.1345	334	0.1201	6372	X-RAY DIFFRACTION	100
4.68-5.9	0.1342	337	0.135	6368	X-RAY DIFFRACTION	99.99
5.9-46.48	0.1736	330	0.1534	6334	X-RAY DIFFRACTION	99.54

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	4.65684092801	0.337842017331	-1.50144501851	2.68519755657	0.71564935549	1.8410980074	-0.0519089962387	-0.0709327530438	-0.166883089772	0.289087508852	-0.0157171422004	-0.0780088320309	0.265034087512	0.0170689213842	0.062431449479	0.360325136363	0.037206501669	-0.0440500093735	0.328277721793	0.00740388868799	0.247292372373	48.4474932677	-42.7448901491	13.8922101724
2	8.50693220081	4.90772708618	1.44436899894	4.80431061865	1.12061822405	3.3449275026	0.040411788319	-0.544562912667	-0.389021214377	0.423476287242	-0.272049317601	0.0362795465625	0.423099572463	-0.237854280446	0.211722497629	0.445735649552	0.0497798166005	0.0732888760753	0.257880731353	-0.0413150168998	0.292734446601	41.4548012309	-51.8312522312	14.0865072047
3	3.23641725911	0.648741486551	-1.03467965362	-0.00978965747004	-0.164047454159	0.480511165118	0.0734916427936	0.0773945539381	-0.347270596535	0.133822061233	-0.176446174965	-0.0394916231749	0.108744993644	-0.0401238187109	0.0956903875661	0.480141175897	-0.0230356366004	0.0404446051803	0.392468748648	-0.0402918649426	0.489404170356	49.6710034583	-53.8306913571	2.56629978753
4	2.9897435191	-2.84503087657	-1.73372240542	5.32002345068	2.43096156032	2.79017707921	-0.0945823600313	-0.109820784317	0.334120692644	0.242004443355	0.10909512882	-0.315824282006	0.101827923615	0.078927260427	-0.0535418652547	0.313267706539	-0.0450779746599	-0.0109153773992	0.348014765681	0.0181108450202	0.350293207196	62.2871722765	-37.0321539785	-7.39739944471
5	1.21877004402	-0.384358993739	-0.226522446477	0.928187454069	0.192174177372	0.388622071959	-0.00205624917495	0.050003368797	0.0672028083758	-0.0402946258181	-0.0324658423622	0.00800974343252	-0.0419339851054	-0.0232688205388	0.0410263461409	0.3511659033	-0.00394237232212	-0.010522275979	0.37470435041	0.00917003549893	0.347098756328	58.9511357438	-33.0310289851	-10.8601936135
6	0.102160742319	0.192712797057	-0.281380416425	0.934803315887	0.37170528282	0.862737079913	0.0205241900532	-0.130685471968	-0.0274051923965	0.0136137777672	-0.166906084031	0.235075235296	0.0833011490641	-0.0851010385514	0.160128973088	0.376609173863	-0.0129390554182	-0.00285009463329	0.352730884589	-0.0302879338295	0.394454761058	38.1032428032	-46.6507780457	-2.07891194008
7	1.43450219025	0.366976837866	-0.0336875381432	1.47954077427	0.0457448857306	0.665835631793	0.0748397281202	-0.0661929310802	0.173189370288	0.0789792315973	-0.147528139025	0.213107470279	-0.0808339689731	-0.0787799135622	0.0690716921968	0.296864004134	0.0139595040267	0.016043970169	0.337386917727	-0.0604989971686	0.375441431126	39.5465400283	-26.6300956189	7.06848491492
8	5.72489511879	-6.52603089518	2.06866748199	8.82023287869	-2.85777850085	2.76949194665	0.0443856714269	-0.0165330641138	0.431059493643	-0.264980237834	-0.0345098638401	-0.390464886809	-0.126782951285	0.0982624934037	0.0139174946531	0.302711930662	-0.0657032570551	-0.00689058279416	0.347942216929	-0.00412157425501	0.32273880459	66.3775802507	-25.789877416	-7.83411641059
9	1.75501709988	0.494506250055	-1.02943309974	0.877637483078	1.28531899094	4.19440086208	0.243572639966	0.146186658755	0.0823199911129	-0.763654789951	-0.206230160455	-0.323042917764	-0.0840643846785	0.218570453343	0.00943181852116	0.286124582929	-0.0676388581551	0.0641945774029	0.480172940979	0.0960703269998	0.422800455422	73.5226020341	-32.8662809105	-18.8658012767
10	4.99762727934	0.996450537364	-1.01714162445	2.7710921917	0.0820022823532	1.00255621771	0.225830755391	0.0508509509404	1.00292662451	0.14365582999	-0.063524369424	0.211735397532	-0.38956340089	-0.0628635370691	-0.204133823276	0.505791968924	0.0373201858614	-0.0172026814132	0.359051496688	-0.0181558381882	0.516850885403	44.284890741	-8.59082593325	2.11883588787
11	1.73829907974	-0.111761655741	-0.600729417661	3.63445404369	1.20845464924	1.82793621617	0.0546890481925	0.235616433513	-0.00178059549237	-0.0735492002763	-0.0914273037555	0.195002568691	-0.0732817526062	-0.447398739023	0.0353010317165	0.343925599608	0.0403913729366	-0.0275318107417	0.427316528578	0.0132947238263	0.203753163987	19.8347494129	-11.7222418087	-56.999760385
12	3.46118314089	3.38422928547	-1.12520891077	7.85195395637	-2.06495990148	2.50988603639	-0.139799931365	0.467875009242	-0.139562274294	-0.525489522216	0.0611218435007	0.295648748668	0.194863785095	-0.474574867719	0.0679122828204	0.317568129394	0.0222610750292	-0.0294365981133	0.55650184026	-0.0844338322661	0.32724817089	11.2069272219	-19.0342217788	-57.3259393466
13	0.0640334629741	0.317037440435	0.250907509367	4.14227679305	1.32935931048	1.0741291286	-0.0432139705453	0.113455227969	-0.0205683485912	-0.0646846311262	0.0911208340909	0.206416018994	-0.00878864091536	-0.144669403302	-0.0183519735221	0.337339715287	-0.0294121040152	0.0201018003439	0.535790273098	-0.0183077712905	0.450264886182	8.6437579465	-11.1132808388	-45.8205762696
14	6.61285318276	-3.82894208212	-2.2224347176	3.00229102212	1.88667276508	2.31160799962	0.300307425431	0.321580927014	0.277579050672	-0.104620259642	-0.168767721465	-0.299972067041	-0.139206246921	-0.0863174996106	-0.168375197358	0.326488583397	-0.0375237848911	-0.0376874920984	0.283562910185	-0.005151768473	0.273308165865	24.8799745834	1.8313802733	-35.7685913917
15	0.533581032011	-0.365605411622	-0.617868404239	1.06744982645	0.681191694325	0.943858747226	0.0508915252063	0.0323314121491	0.0322367601097	0.0543406305168	-0.0171036983764	-0.0589040991394	-0.00447869295564	-0.00846037263235	-0.0275040467961	0.363822073217	-0.0143068632981	-0.0363826623512	0.334690364353	0.00305799191685	0.300583490822	26.7229971651	-2.03657409972	-32.1917529283
16	2.08819573735	-0.102309193209	-0.405528068569	1.20573953594	0.274749627505	1.37985354971	-0.0601262501538	-0.00884164352983	-0.257161970277	0.0167871868996	-0.0186845304407	-0.0781650111074	0.17898508937	-0.116181194297	0.084241111118	0.319410986934	-0.00379923494177	0.0162874583991	0.287496946909	-0.0325797711799	0.296939092719	29.589784269	-24.4812551698	-47.6388568754
17	0.664213595098	-0.182767032757	-0.695486255088	1.04029757771	0.904606817282	3.67148146741	0.0333591570832	-0.0617088598678	0.159302005623	0.0283499343289	0.104046599272	-0.317038817711	0.0683594971288	0.398463075443	-0.165934840742	0.300775313214	-0.0297293672687	-0.00328444916489	0.377786665335	-0.0453544010519	0.480117728638	44.8231161594	-3.38551393647	-41.2081667801
18	0.669373957825	0.31629645157	-1.06413652561	1.88532302814	0.443487964569	5.89845682088	0.206544351212	0.0163816824679	0.168415203953	-0.212096847533	-0.0823066872815	0.0276692488066	-0.692963682553	-0.425998489956	-0.0955508711518	0.495619678397	0.0398364236749	0.0118711178145	0.296645679852	-0.0226603421564	0.380088840974	19.6560806183	17.0514068638	-31.8310166006
19	4.29721389661	-3.36025621676	-4.40983254321	4.87236376522	5.65519142869	6.68535290807	0.391234012835	-0.539734001126	0.745237874663	-0.256264970276	0.603198235899	-1.01867291041	-0.547455307632	0.905131163479	-1.12702927485	0.412372215442	-0.068509312743	-0.0289400382859	0.484317548667	-0.0885634184324	0.554994286194	47.8723307952	4.21804269979	-32.071303646
20	5.91308736147	1.73605781432	0.132612748663	4.76971871748	0.261621301896	1.85072056133	-0.173469388979	0.206205844172	-0.525023837128	0.0564308880375	0.452800650122	-1.48224570302	0.0468243183484	0.395972044623	-0.245450008057	0.413200087511	0.0695509074465	0.0221661213987	0.453277987853	-0.131358932643	0.673998984676	53.8462882759	-20.1408751198	-44.7003230292

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 199 )	A	A	149 - 199	149 - 199
5	5	chain 'A' and (resid 200 through 319 )	A	A	200 - 319	200 - 319
6	6	chain 'A' and (resid 320 through 375 )	A	A	320 - 375	320 - 375
7	7	chain 'A' and (resid 376 through 504 )	A	A	376 - 504	376 - 504
8	8	chain 'A' and (resid 505 through 548 )	A	A	505 - 548	505 - 548
9	9	chain 'A' and (resid 549 through 585 )	A	A	549 - 585	549 - 585
10	10	chain 'A' and (resid 586 through 655 )	A	A	586 - 655	586 - 637
11	11	chain 'B' and (resid 1 through 75 )	B	F	1 - 75	1 - 75
12	12	chain 'B' and (resid 76 through 113 )	B	F	76 - 113	76 - 113
13	13	chain 'B' and (resid 114 through 148 )	B	F	114 - 148	114 - 148
14	14	chain 'B' and (resid 149 through 199 )	B	F	149 - 199	149 - 199
15	15	chain 'B' and (resid 200 through 334 )	B	F	200 - 334	200 - 334
16	16	chain 'B' and (resid 335 through 479 )	B	F	335 - 479	335 - 479
17	17	chain 'B' and (resid 480 through 530 )	B	F	480 - 530	480 - 530
18	18	chain 'B' and (resid 531 through 568 )	B	F	531 - 568	531 - 568
19	19	chain 'B' and (resid 569 through 601 )	B	F	569 - 601	569 - 601
20	20	chain 'B' and (resid 602 through 655 )	B	F	602 - 655	602 - 638

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 641 molecules

-
Details

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 641 molecules

-Details

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 641 molecules

-
Details

-
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