PDB-8db0: Crystal structure of DMATS1 prenyltransferase in complex with L-T...

ID or keywords:

Entry

Database: PDB / ID: 8db0

Title

Crystal structure of DMATS1 prenyltransferase in complex with L-Trp and DMSPP

Components

Dimethylallyltryptophan synthase 1

Keywords

TRANSFERASE / prenyltransferase / fungal protein / DMATS

Function / homology

Function and homology information

alkaloid metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity
Similarity search - Function

Biological species

Fusarium fujikuroi (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.26 Å

Authors

Eaton, S.A. / Ronnebaum, T.A. / Roose, B.W. / Christianson, D.W.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2022
Title: Structural Basis of Substrate Promiscuity and Catalysis by the Reverse Prenyltransferase N -Dimethylallyl-l-tryptophan Synthase from Fusarium fujikuroi .
Authors: Eaton, S.A. / Ronnebaum, T.A. / Roose, B.W. / Christianson, D.W.

History

Deposition	Jun 14, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 5, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8db0.cif.gz	700.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8db0.ent.gz	519.5 KB	Display	PDB format
PDBx/mmJSON format	8db0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8db0_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	8db0_full_validation.pdf.gz	2.2 MB	Display
Data in XML	8db0_validation.xml.gz	57.8 KB	Display
Data in CIF	8db0_validation.cif.gz	80.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/db/8db0 ftp://data.pdbj.org/pub/pdb/validation_reports/db/8db0	HTTPS FTP

-
Related structure data

Related structure data	8dayC 8dazC 8db1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Dimethylallyltryptophan synthase 1

B: Dimethylallyltryptophan synthase 1

C: Dimethylallyltryptophan synthase 1

D: Dimethylallyltryptophan synthase 1

hetero molecules

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

1

A: Dimethylallyltryptophan synthase 1

hetero molecules

defined by author
Evidence: gel filtration
47.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dimethylallyltryptophan synthase 1

hetero molecules

defined by author
Evidence: gel filtration
47.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Dimethylallyltryptophan synthase 1

hetero molecules

defined by author
47.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Dimethylallyltryptophan synthase 1

hetero molecules

defined by author
47.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.500, 108.400, 182.040
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
1	1
2	1
3	1
4	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	PRO	PRO	(chain 'A' and (resid 11 through 13 or (resid 14...	A	A	11 - 156	11 - 156
1	2	GLY	GLY	SER	SER	(chain 'A' and (resid 11 through 13 or (resid 14...	A	A	170 - 211	170 - 211
1	3	LEU	LEU	THR	THR	(chain 'A' and (resid 11 through 13 or (resid 14...	A	A	216 - 271	216 - 271
1	4	ARG	ARG	PRO	PRO	(chain 'A' and (resid 11 through 13 or (resid 14...	A	A	276 - 307	276 - 307
1	5	HIS	HIS	ASP	ASP	(chain 'A' and (resid 11 through 13 or (resid 14...	A	A	311 - 321	311 - 321
1	6	GLN	GLN	ALA	ALA	(chain 'A' and (resid 11 through 13 or (resid 14...	A	A	327 - 411	327 - 411
2	1	SER	SER	PRO	PRO	(chain 'B' and (resid 11 through 13 or (resid 14...	B	B	11 - 156	11 - 156
2	2	GLY	GLY	SER	SER	(chain 'B' and (resid 11 through 13 or (resid 14...	B	B	170 - 211	170 - 211
2	3	LEU	LEU	THR	THR	(chain 'B' and (resid 11 through 13 or (resid 14...	B	B	216 - 271	216 - 271
2	4	ARG	ARG	PRO	PRO	(chain 'B' and (resid 11 through 13 or (resid 14...	B	B	276 - 307	276 - 307
2	5	HIS	HIS	ASP	ASP	(chain 'B' and (resid 11 through 13 or (resid 14...	B	B	311 - 321	311 - 321
2	6	GLN	GLN	ALA	ALA	(chain 'B' and (resid 11 through 13 or (resid 14...	B	B	327 - 411	327 - 411
3	1	SER	SER	PRO	PRO	(chain 'C' and (resid 11 through 24 or (resid 25...	C	C	11 - 156	11 - 156
3	2	GLY	GLY	SER	SER	(chain 'C' and (resid 11 through 24 or (resid 25...	C	C	170 - 211	170 - 211
3	3	LEU	LEU	THR	THR	(chain 'C' and (resid 11 through 24 or (resid 25...	C	C	216 - 271	216 - 271
3	4	ARG	ARG	PRO	PRO	(chain 'C' and (resid 11 through 24 or (resid 25...	C	C	276 - 307	276 - 307
3	5	HIS	HIS	ASP	ASP	(chain 'C' and (resid 11 through 24 or (resid 25...	C	C	311 - 321	311 - 321
3	6	GLN	GLN	ALA	ALA	(chain 'C' and (resid 11 through 24 or (resid 25...	C	C	327 - 411	327 - 411
4	1	SER	SER	PRO	PRO	(chain 'D' and (resid 11 through 72 or (resid 73...	D	D	11 - 156	11 - 156
4	2	GLY	GLY	SER	SER	(chain 'D' and (resid 11 through 72 or (resid 73...	D	D	170 - 211	170 - 211
4	3	LEU	LEU	THR	THR	(chain 'D' and (resid 11 through 72 or (resid 73...	D	D	216 - 271	216 - 271
4	4	ARG	ARG	PRO	PRO	(chain 'D' and (resid 11 through 72 or (resid 73...	D	D	276 - 307	276 - 307
4	5	HIS	HIS	ASP	ASP	(chain 'D' and (resid 11 through 72 or (resid 73...	D	D	311 - 321	311 - 321
4	6	GLN	GLN	ALA	ALA	(chain 'D' and (resid 11 through 72 or (resid 73...	D	D	327 - 411	327 - 411

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Dimethylallyltryptophan synthase 1 / DMATS 1 / DMATS1 biosynthesis cluster protein DMATS1 Mass: 47341.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium fujikuroi (fungus) / Gene: DMATS1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: S0EH60, Transferases; Transferring alkyl or aryl groups, other than methyl groups

#1: Protein

Dimethylallyltryptophan synthase 1 / DMATS 1 / DMATS1 biosynthesis cluster protein DMATS1

Mass: 47341.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Fusarium fujikuroi (fungus) / Gene: DMATS1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: S0EH60, Transferases; Transferring alkyl or aryl groups, other than methyl groups

-
Non-polymers , 5 types, 464 molecules

#2: 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
#3: Chemical	ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₉
#4: Chemical	ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₂O₆P₂S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.27 Å³/Da / Density % sol: 46 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 7.5 mg/mL protein, 0.1 M Tris-HCl (pH 8.9), 0.55 M NaCl, 25% (v/v) PEG 3,350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.26→93.14 Å / Num. obs: 84491 / % possible obs: 100 % / Redundancy: 7.8 % / B_iso Wilson estimate: 39.58 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.21 / R_pim(I) all: 0.079 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.26→2.3 Å / R_merge(I) obs: 2.19 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4417 / CC_1/2: 0.52 / R_pim(I) all: 1.26 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing
PHENIX	1.14_3260	refinement
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 2.26→93.14 Å / SU ML: 0.2561 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7039 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2324	2000	2.37 %
R_work	0.2062	157835	-
obs	0.2068	84364	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 63.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.26→93.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11903	0	117	456	12476

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0047	12385
X-RAY DIFFRACTION	f_angle_d	0.778	16959
X-RAY DIFFRACTION	f_chiral_restr	0.0517	1852
X-RAY DIFFRACTION	f_plane_restr	0.0054	2175
X-RAY DIFFRACTION	f_dihedral_angle_d	18.8713	4246

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 (%)
2.26-2.29	0.2767	138	0.2936	5721	X-RAY DIFFRACTION	99.22
2.29-2.32	0.3313	143	0.2809	5933	X-RAY DIFFRACTION	99.79
2.32-2.35	0.3197	141	0.2839	5807	X-RAY DIFFRACTION	99.6
2.35-2.38	0.3205	141	0.2837	5822	X-RAY DIFFRACTION	99.9
2.38-2.42	0.2752	142	0.2643	5871	X-RAY DIFFRACTION	99.87
2.42-2.46	0.2841	142	0.2608	5844	X-RAY DIFFRACTION	99.88
2.46-2.5	0.2973	147	0.2517	5854	X-RAY DIFFRACTION	99.97
2.5-2.54	0.2655	140	0.2573	5836	X-RAY DIFFRACTION	99.83
2.54-2.59	0.2967	143	0.2538	5874	X-RAY DIFFRACTION	99.85
2.59-2.64	0.2777	144	0.2494	5844	X-RAY DIFFRACTION	99.83
2.64-2.69	0.3071	139	0.2549	5807	X-RAY DIFFRACTION	99.75
2.69-2.75	0.2825	145	0.2524	5858	X-RAY DIFFRACTION	99.65
2.75-2.81	0.2832	144	0.2451	5862	X-RAY DIFFRACTION	99.78
2.81-2.88	0.2854	144	0.2442	5822	X-RAY DIFFRACTION	99.47
2.88-2.96	0.2261	140	0.2336	5790	X-RAY DIFFRACTION	99.81
2.96-3.05	0.2692	143	0.221	5901	X-RAY DIFFRACTION	99.98
3.05-3.15	0.2472	141	0.2247	5835	X-RAY DIFFRACTION	99.93
3.15-3.26	0.2584	144	0.2172	5868	X-RAY DIFFRACTION	99.97
3.26-3.39	0.2613	146	0.2105	5861	X-RAY DIFFRACTION	99.92
3.39-3.54	0.2063	136	0.1912	5855	X-RAY DIFFRACTION	99.9
3.54-3.73	0.2069	142	0.1851	5865	X-RAY DIFFRACTION	99.93
3.73-3.96	0.2094	141	0.1815	5847	X-RAY DIFFRACTION	99.95
3.96-4.27	0.1778	138	0.1684	5853	X-RAY DIFFRACTION	99.65
4.27-4.7	0.1884	132	0.1511	5872	X-RAY DIFFRACTION	99.88
4.7-5.38	0.1808	145	0.1621	5825	X-RAY DIFFRACTION	99.92
5.38-6.78	0.2499	137	0.2058	5882	X-RAY DIFFRACTION	99.95
6.78-93.14	0.1889	134	0.1891	5826	X-RAY DIFFRACTION	99.62

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	3.26198924322	-0.0846038567501	-1.47960394507	2.4784538479	-0.350615377436	2.64029664015	0.0494933575859	-0.0856151416456	0.0734660463492	0.125389703016	0.0363582754957	0.363880734092	-0.214182333054	-0.0854516210011	-0.104063208906	0.265222575562	0.0378701402666	0.0215732141724	0.247737245569	0.0852412741832	0.234650427133	18.1946614567	-2.61441861497	-16.0069229985
2	8.61240759864	-0.425948380644	3.62996429095	2.79393743725	2.50461277449	7.1344510138	-0.100159494089	0.257191388588	-1.0505275578	-0.0512737921404	0.0433849718403	1.167298594	-0.0547082550964	-0.530627403905	0.142253346505	0.288817022939	0.00263884187787	0.0405392083604	0.461925352145	0.00665423571215	0.788849192728	3.94186826883	-17.4786086085	-18.6257460891
3	3.92849531823	0.998322206564	-0.259343059925	5.04041095214	0.353895643693	2.58305901932	-0.242843047017	0.302715759472	-1.19207999078	-0.188090386553	-0.0040766628515	0.640358423177	0.446256630216	-0.619188140269	0.256089247291	0.27082830749	-0.0356324605282	0.0607515643018	0.386566013672	-0.0124128281695	0.815882529116	10.0052661467	-20.659195348	-19.7186418365
4	1.40999275083	-0.891246042857	-1.74266284955	6.73453522342	1.31304874485	1.88195972114	-0.651611956336	0.312343222816	-2.09443350482	-0.24093604974	0.135722886926	0.503491313232	0.723703077928	-1.23663228825	0.404882900327	0.525203512799	-0.223254357813	0.286911922681	0.235404862578	-0.0417018479751	1.47767096204	13.9585645398	-32.8973227965	-22.6265685808
5	4.78866377019	0.230518010076	-2.55166796029	2.5065172086	0.476510517988	1.46004514447	-0.318463726919	0.408677799366	-1.4537421712	-0.281671543194	-0.216283969358	0.428184932	0.441351158945	-0.100488158238	0.483851177457	0.41036331476	0.0188966521698	0.0708559528781	0.317212616731	-0.0593076543383	0.662873445826	26.4533269619	-29.3175554464	-24.1608937433
6	2.52331902736	0.0139285214338	-1.00267858485	4.14815320921	1.48983690191	4.37310763641	-0.351283945258	-0.134736609257	-0.84557010082	0.0726014007602	-0.0660795174568	0.0325026891533	0.49255431577	0.173268745955	0.387386858522	0.292178116311	0.0462019641575	0.139992541667	0.290846180089	0.165130557097	0.535834598031	28.7203581052	-27.8412190704	-16.9618547236
7	3.53042131755	-0.597145373934	-0.617292798222	3.40850557675	0.135089084019	0.340088875251	-0.0856101765834	-0.0706540111055	-0.0514907829802	0.0967213229502	0.00818739128217	-0.114473580077	-0.0189273098034	0.228010089546	0.0509444718664	0.231567835097	0.0262977478518	0.0220584809529	0.348020850358	0.117015111306	0.200089770038	34.4724095209	-13.4929725409	-18.5912166323
8	3.48067790298	-0.971121492789	1.20759757831	2.70373056169	0.256727401501	2.51121749629	0.0567699344478	0.0914717396529	0.0670946095929	-0.178286907109	-0.00560004264281	0.178294801758	-0.0677902153281	-0.099051797455	-0.046164027014	0.193319406847	-0.0306403241059	0.0193506802071	0.193969057392	-0.0153335473106	0.219321963753	20.3366031712	39.2888313891	-77.2394778521
9	4.5669825591	-0.99943866199	0.43559732249	8.92647881301	-1.48467771968	4.27682878458	-0.0223520263744	-0.158130830354	0.402019890934	-0.317865474586	0.229680643295	0.692465001223	-0.514397610406	-0.425369375764	-0.131820498077	0.234618813821	-0.00762872135695	0.0233336525861	0.286145927084	-0.0470330852541	0.374785798494	13.5239641674	52.1638248937	-77.0729006542
10	4.08368001238	0.0114574764849	1.14156550628	8.09766634611	1.07327139265	2.71814459716	-0.247586701416	-0.318818616252	1.4250240094	0.434994878788	-0.000539963742791	0.619728862689	-0.917919693988	-0.423041122869	0.221644950292	0.519522945623	0.120787606267	-0.0699782881201	0.374092720688	-0.114553961715	0.72130325918	13.3730095188	66.8467760325	-72.4752125438
11	5.50132833673	-0.403159545748	1.08556455353	2.06584429301	0.538296637796	0.456534969759	-0.272725996301	-0.402977029041	1.03378281685	0.125926550988	0.0433704003064	-0.347674059624	-0.491862702387	0.0396188567968	0.186153319419	0.524618672424	-0.0110830447397	-0.0368772817311	0.372609064283	-0.151405476566	0.643188278094	28.0866327045	64.44611149	-68.7385167095
12	9.04205961332	-1.06974879974	-1.40595739088	6.77199529357	2.52764600143	4.661018421	0.0705229433629	0.386162261847	1.16633834822	-0.620153751047	0.125812526933	-0.210529827553	-0.90709726159	0.16702159922	-0.158341220497	0.516457379463	-0.0367680741119	-0.0846457642247	0.258297321011	-0.0181225310845	0.540624112117	30.9564483142	62.9246234258	-74.92082224
13	5.83254510463	-0.0393922453155	0.586682936954	5.47496326883	-1.03386470183	2.49537878727	-0.23226789272	0.228410679343	0.103538244044	-0.294804000252	0.243578297099	-0.169701648309	-0.114899953917	0.280358930227	0.0098570115004	0.193959051662	-0.0600397100814	-0.00684979455566	0.254136001425	-0.0463708409621	0.258522543566	37.8468577244	49.6037426618	-73.1060879779
14	2.33866420494	-0.410551865147	0.140357667684	5.37969941297	0.944116584989	2.93442270136	0.261884186122	-0.0743899559183	-0.163848981366	0.185921383862	-0.0325798639038	0.470975299763	0.560603741911	-0.347273101688	-0.226000925804	0.432965455606	-0.0755695314465	-0.0754559047634	0.319467646112	0.110019220728	0.320226625262	18.6595108333	7.89230445154	-69.4404466908
15	3.98444414984	-0.450655972728	-1.99989207051	7.75994368195	-1.80339008803	1.73463352999	0.336145080951	0.0238864469165	-0.400722949289	-0.0859250338773	-0.0193409778566	-0.113145909562	1.29352386247	-0.0197877650996	-0.348616781924	0.830276663183	-0.00811241951817	-0.278398988437	0.433856739914	0.0840879770909	0.427880808201	22.6690969814	-5.43690370632	-73.9866247352
16	3.76312797957	-1.34438993178	0.855473880876	3.80641461006	-2.52882447786	3.43428924475	0.695990209719	-0.111403359356	-1.76031553493	-1.08320107878	-0.451859252004	-0.629990312873	1.48972282157	0.662945664566	-0.181385095838	1.61763985949	0.28484723961	-0.501708541893	0.297347125132	-0.0460416432803	1.10130265713	31.467395683	-19.2644141082	-72.6093552402
17	0.367577583398	-0.798406006976	0.92238340274	2.82325354847	-0.584952230038	2.47226686597	0.358320399889	-0.870256513917	-1.23772435277	0.341874116249	-0.0710406308882	-0.0397799916523	1.04112320155	-0.154709974399	-0.330608505274	1.08678693696	-0.193364928027	-0.401383624949	0.8935926561	0.475283232916	0.944832541749	27.149155604	-14.7998424302	-56.1353161377
18	2.70521103933	-1.61510840112	-0.152914680486	3.6569307572	-0.966952866687	4.06439704127	0.761106057752	-0.385737887321	-0.333423224056	0.683210686791	-0.3125819752	-0.0537382123932	0.841691827902	-0.134829490688	-0.178537694931	1.23730685244	-0.325931695304	-0.499460836985	0.706677548945	0.44459301462	0.558132205642	25.196571063	-10.8370339024	-57.632504333
19	1.52387643564	-1.33579925246	1.41967536587	3.95111521582	-1.06861174834	3.92786620995	0.258563597866	-1.7366185214	-0.615447305571	0.614364556592	0.504162291647	0.451983149037	0.218514708613	-0.564195320446	-0.660871324137	0.789190966056	-0.166688299574	-0.114278236438	1.03521237936	0.27936140633	0.484418109997	21.2004236873	1.33424227339	-50.0458006242
20	2.1801743276	0.201656051226	0.903352133624	5.16325175783	-1.02652173985	1.516886055	0.369221385824	-0.152083885173	0.296362373706	0.517044865163	0.209734396407	1.27994733132	-0.179341043967	-0.508691883884	-0.623166805607	0.735347010485	0.0459917998923	0.24051345563	0.552606661702	0.323950554131	0.983455080589	12.9573621465	25.4131520151	-28.9181000479
21	2.78248233444	0.0370643772265	0.295674787961	4.0081912012	-0.164965132912	1.25096111755	0.493227455499	-0.499780983017	1.07770058276	1.44708021523	-0.0914055015261	0.201433487499	-1.11071449668	0.313218359779	-0.419406522702	1.51755527652	-0.0835368148518	0.451373945171	0.559554073254	-0.0212802884422	1.05522195662	22.0196757904	43.58609748	-20.6488778953
22	2.3670633793	0.71938870356	-0.808163703264	4.74200682248	-1.96208258864	4.37710572405	0.188410346323	0.683397150589	1.04135795697	-0.217529140843	0.57253372462	1.19254551479	-0.393742464995	-0.0533687978505	-0.693380417765	0.763474035992	0.0583297368671	0.21200999952	0.657078448836	0.358902266335	0.981313790558	22.9373773423	41.6434925257	-42.8723972825

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 137 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 138 through 172 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 173 through 211 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 212 through 243 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 244 through 294 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 295 through 343 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 344 through 414 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 11 through 153 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 154 through 199 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 200 through 243 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 244 through 294 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 295 through 343 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 344 through 412 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 11 through 153 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 154 through 199 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 200 through 227 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 228 through 315 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 316 through 343 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 344 through 412 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 11 through 124 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 125 through 262 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 263 through 412 )

-
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://pdbjlvh1.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, 4 molecules ABCD

-
Non-polymers , 5 types, 464 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, 4 molecules ABCD

-Non-polymers , 5 types, 464 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, 4 molecules ABCD

-
Non-polymers , 5 types, 464 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