PDB-6vzr: Engineered TTLL6 bound to the initiation analog

ID or keywords:

Entry

Database: PDB / ID: 6vzr

Title

Engineered TTLL6 bound to the initiation analog

Components

(TTLL6 unregistered ...) x 2
Tubulin polyglutamylase TTLL6

Keywords

LIGASE / TTLL6 /

protein engineering / glutamylation / phosphinic acid based inhibitor

Function / homology

Function and homology information

positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / regulation of cilium beat frequency involved in ciliary motility / 9+0 non-motile cilium / microtubule severing /

Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / microtubule bundle formation ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Mahalingan, K.K. / Keenen, E.K. / Strickland, M. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	ZIA NS 003163	United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	ZIA NS003122	United States

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes.
Authors: Mahalingan, K.K. / Keith Keenan, E. / Strickland, M. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.

History

Deposition	Feb 28, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 10, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6vzr.cif.gz	679.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6vzr.ent.gz	557.1 KB	Display	PDB format
PDBx/mmJSON format	6vzr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/6vzr ftp://data.pdbj.org/pub/pdb/validation_reports/vz/6vzr	HTTPS FTP

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Related structure data

Related structure data	6vzqC 6vzsC 6vztC 6vzuC 6vzvC 6vzwC 4ylrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2b11-1 6vzs-2 1wam-d 2evh-d 5olq-1 6vzs-1 2wo6-2 2nt0-1 2pcb-1 2evj-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tubulin polyglutamylase TTLL6

B: Tubulin polyglutamylase TTLL6

C: Tubulin polyglutamylase TTLL6

D: Tubulin polyglutamylase TTLL6

F: TTLL6 unregistered chain

G: TTLL6 unregistered chain

hetero molecules

222 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tubulin polyglutamylase TTLL6

G: TTLL6 unregistered chain

hetero molecules

defined by author
Evidence: gel filtration
56 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tubulin polyglutamylase TTLL6

hetero molecules

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

3

C: Tubulin polyglutamylase TTLL6

hetero molecules

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

4

D: Tubulin polyglutamylase TTLL6

F: TTLL6 unregistered chain

hetero molecules

defined by author
55.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.099, 108.813, 171.618
Angle α, β, γ (deg.)	90.00, 90.03, 90.00
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	(CHAIN 'A' AND (RESID 57 THROUGH 102 OR (RESID 103...
2	1	1	(CHAIN 'B' AND (RESID 57 THROUGH 98 OR (RESID 99...
3	1	1	(CHAIN 'C' AND (RESID 57 THROUGH 98 OR (RESID 99...
4	1	1	(CHAIN 'D' AND (RESID 57 THROUGH 98 OR (RESID 99...
1	1	2	(CHAIN 'F' AND RESID 8 THROUGH 18)
2	1	2	CHAIN 'G'

NCS ensembles :

ID
1
2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Tubulin polyglutamylase TTLL6 / Tubulin--tyrosine ligase-like protein 6 Mass: 53345.398 Da / Num. of mol.: 4 / Mutation: Q180R,C179A,H362I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Q9E8, Ligases

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TTLL6 unregistered ... , 2 types, 2 molecules FG

#2: Protein/peptide	TTLL6 unregistered chain Mass: 1039.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Unregistered part of one of the chains A,B,C,D / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli)
#3: Protein/peptide	TTLL6 unregistered chain Mass: 954.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Unregistered part of one of the chains A,B,C,D / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 424 molecules

#4: Chemical	ChemComp-2TI / (2~{S})-2-[[[(3~{R})-3-acetamido-4-(ethylamino)-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid Mass: 460.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₆N₂O₁₁P₂
#5: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#6: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.26 Å³/Da / Density % sol: 66.54 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 100 mM Sodium Citrate, 200 mM MgCl2, 8-12% Peg 20000 PH range: 6.0-6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97741 Å / Relative weight: 1
Reflection	Resolution: 2.6→45.95 Å / Num. obs: 169504 / % possible obs: 99.73 % / Redundancy: 2 % / B_iso Wilson estimate: 42.38 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.0418 / R_pim(I) all: 0.0418 / R_rim(I) all: 0.05917 / Net I/σ(I): 10.45
Reflection shell	Resolution: 2.6→2.693 Å / Redundancy: 2 % / R_merge(I) obs: 0.312 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 16567 / CC_1/2: 0.864 / CC star: 0.963 / R_pim(I) all: 0.312 / R_rim(I) all: 0.4412 / % possible all: 99.07

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YLR

4ylr

Resolution: 2.6→45.95 Å / SU ML: 0.315 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.458
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2

	R_factor	Num. reflection	% reflection
R_free	0.249	8290	4.98 %
R_work	0.23	-	-
obs	0.231	166316	99.6 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→45.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12638	0	388	382	13408

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13356
X-RAY DIFFRACTION	f_angle_d	0.512	18108
X-RAY DIFFRACTION	f_dihedral_angle_d	14.26	7862
X-RAY DIFFRACTION	f_chiral_restr	0.038	1972
X-RAY DIFFRACTION	f_plane_restr	0.003	2285

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type
1	1	A	X-RAY DIFFRACTION	POSITIONAL
1	2	B	X-RAY DIFFRACTION	POSITIONAL
1	3	C	X-RAY DIFFRACTION	POSITIONAL
1	4	D	X-RAY DIFFRACTION	POSITIONAL
2	1	F	X-RAY DIFFRACTION	POSITIONAL
2	2	G	X-RAY DIFFRACTION	POSITIONAL

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 (%)
2.6-2.63	0.3895	253	0.3228	4988	X-RAY DIFFRACTION	96
2.63-2.66	0.3824	242	0.3382	5348	X-RAY DIFFRACTION	100
2.66-2.69	0.3303	288	0.323	5244	X-RAY DIFFRACTION	100
2.69-2.73	0.3333	279	0.2919	5306	X-RAY DIFFRACTION	100
2.73-2.76	0.3049	297	0.2865	5277	X-RAY DIFFRACTION	100
2.76-2.8	0.3061	276	0.2824	5230	X-RAY DIFFRACTION	100
2.8-2.84	0.3139	306	0.2807	5311	X-RAY DIFFRACTION	100
2.84-2.88	0.3285	336	0.2882	5273	X-RAY DIFFRACTION	100
2.88-2.93	0.313	274	0.271	5226	X-RAY DIFFRACTION	100
2.93-2.98	0.2869	259	0.2495	5312	X-RAY DIFFRACTION	100
2.98-3.03	0.2716	234	0.2487	5307	X-RAY DIFFRACTION	100
3.03-3.08	0.2492	216	0.2462	5348	X-RAY DIFFRACTION	100
3.08-3.14	0.2693	260	0.2478	5298	X-RAY DIFFRACTION	100
3.14-3.21	0.2883	282	0.25	5246	X-RAY DIFFRACTION	100
3.21-3.28	0.2676	282	0.2404	5337	X-RAY DIFFRACTION	100
3.28-3.35	0.2588	287	0.2445	5201	X-RAY DIFFRACTION	100
3.35-3.44	0.2333	265	0.236	5305	X-RAY DIFFRACTION	100
3.44-3.53	0.2808	262	0.2286	5286	X-RAY DIFFRACTION	100
3.53-3.63	0.2364	318	0.2223	5258	X-RAY DIFFRACTION	100
3.63-3.75	0.2333	284	0.2284	5297	X-RAY DIFFRACTION	100
3.75-3.88	0.2623	248	0.2184	5327	X-RAY DIFFRACTION	100
3.88-4.04	0.2505	294	0.2133	5256	X-RAY DIFFRACTION	100
4.04-4.22	0.1911	298	0.1895	5231	X-RAY DIFFRACTION	100
4.22-4.45	0.2053	261	0.1843	5301	X-RAY DIFFRACTION	100
4.45-4.72	0.1778	293	0.1691	5299	X-RAY DIFFRACTION	100
4.72-5.09	0.1811	256	0.1876	5281	X-RAY DIFFRACTION	100
5.09-5.6	0.2468	256	0.2169	5292	X-RAY DIFFRACTION	100
5.6-6.41	0.2441	293	0.2469	5302	X-RAY DIFFRACTION	100
6.41-8.07	0.2524	315	0.233	5218	X-RAY DIFFRACTION	100
8.07-45.95	0.221	276	0.2124	5121	X-RAY DIFFRACTION	97

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	5.0704	0.1075	1.8944	6.9089	-2.5582	2.3044	0.1953	0.8658	-0.08	-1.0915	-0.0694	0.9679	0.1866	-0.5507	-0.1913	0.4719	0.086	-0.1166	0.5161	0.0731	0.4067	-2.0775	27.1035	65.4361
2	2.4815	-0.2045	-0.3503	2.946	-0.157	3.3371	0.0655	0.2492	-0.4014	-0.5254	0.0122	-0.9901	0.2114	0.5519	-0.0971	0.3294	0.0145	0.1564	0.3478	0.0056	0.6861	28.4322	11.4871	69.3274
3	2.5568	0.2633	0.5421	2.4832	0.267	1.967	0.016	-0.0635	-0.0375	-0.1947	-0.0744	-0.4632	-0.0614	0.1033	0.03	0.1526	-0.0092	0.0662	0.2068	0.038	0.423	20.4739	24.4569	77.7458
4	2.3652	-0.3056	-0.3874	2.8896	0.9146	2.7696	0.2146	0.4155	0.6876	-1.1687	-0.1298	0.1082	-0.7464	0.0282	-0.0828	0.6825	0.0758	0.0253	0.3699	0.1887	0.5742	10.7436	37.6931	63.6589
5	5.0577	0.6343	1.1766	7.9375	2.4187	9.9589	-0.0388	-0.9995	-0.1897	0.8419	0.1056	-0.6115	0.2504	0.905	-0.0512	0.7024	0.0182	-0.0939	0.8119	-0.0977	0.3487	39.3743	4.7369	20.7384
6	3.3598	0.687	0.6313	4.0541	0.8724	1.7717	0.0695	-0.3671	-0.3721	0.294	-0.0955	0.4954	0.1268	-0.0991	0.0032	0.5487	0.0509	0.0794	0.4566	0.0365	0.3561	12.5108	-7.5491	10.8666
7	4.1863	-0.2298	1.4476	2.5821	0.4758	4.4569	0.0379	-0.4569	0.1243	0.3232	0.005	0.0616	-0.1676	-0.1935	0.0106	0.5475	0.0074	0.1086	0.3655	-0.021	0.2734	17.1024	6.9897	12.2289
8	0.8825	0.2986	0.5818	1.9181	0.5086	1.7021	0.0702	-0.4621	0.2702	0.4617	0.0401	-0.0063	-0.1988	0.055	-0.11	0.7496	0.0112	0.0938	0.6366	-0.0738	0.341	25.3642	13.4201	22.0045
9	4.9726	-0.5867	-2.2169	7.7174	2.0287	9.6339	0.1352	1.0091	0.1342	-0.7766	0.0023	-0.8548	-0.3037	0.9492	-0.1143	0.2959	0.0099	0.0828	0.5676	-0.0964	0.4437	39.5049	-20.9091	65.1144
10	2.0524	-0.4459	0.1872	2.0967	0.4236	2.6398	0.0036	0.5246	0.4719	-0.4666	-0.0878	0.8568	-0.2858	-0.525	0.0606	0.3179	0.0247	-0.1681	0.4108	0.0359	0.766	9.0069	-5.3006	69.3462
11	2.415	0.4167	-0.7597	1.7421	0.0875	2.2501	0.0244	-0.0765	0.0529	-0.0917	-0.0667	0.251	-0.0273	-0.0272	0.024	0.1583	0.0007	-0.0858	0.2269	0.0008	0.473	17.1414	-18.5508	77.9313
12	1.9855	-0.3187	-0.9156	2.7569	0.6873	2.7833	-0.0369	0.5257	-0.2477	-0.5968	0.0171	0.0867	0.3479	-0.0964	-0.0125	0.3817	-0.0195	-0.0816	0.3394	-0.0576	0.4582	25.3214	-29.4549	63.6091
13	1.6932	-1.1988	1.5186	1.8079	-0.1678	8.1828	0.1746	-0.6458	0.0805	1.0502	-0.2473	0.6976	-0.295	-0.708	0.0611	1.0682	-0.1331	0.1386	0.7768	0.0977	0.3465	-1.2497	-43.1716	20.5135
14	2.0673	-0.1469	0.1991	3.6952	0.1007	5.3714	0.1613	-0.4367	0.148	0.757	-0.0584	-0.7318	-0.0577	0.4752	-0.1441	0.613	-0.0146	-0.1795	0.4775	0.0196	0.4282	29.6175	-27.369	15.4866
15	2.6277	-0.0366	-0.2599	2.6814	0.9502	0.5137	0.0437	0.0627	0.059	0.2104	0.0489	-0.236	0.0997	-0.1063	-0.0601	0.6153	0.0073	-0.0292	0.4771	0.0476	0.2495	19.952	-40.9595	7.8785
16	1.6614	0.4402	-1.1984	1.7953	1.0097	1.2761	0.1125	-0.4154	-0.4828	0.9973	-0.1399	-0.087	0.5377	0.017	0.0524	1.1215	-0.0844	-0.0884	0.5947	0.1657	0.369	12.5265	-51.8419	21.3934
17	0.4918	1.9441	-1.5691	8.6728	-6.4485	5.0601	-1.6518	-1.3337	1.3864	1.9815	-0.2363	-1.5226	-3.0302	-0.6193	1.779	1.7065	-0.4763	-0.0913	1.5861	-0.4717	1.0901	17.0644	-41.7911	46.5309
18	0.6671	2.8924	-1.7429	1.9989	-7.5952	4.5845	-2.3081	1.4583	-1.8649	-1.873	-0.2616	-1.2192	2.7297	-0.8434	2.4773	1.7641	0.4669	0.0074	1.4965	-0.4915	1.2624	17.5405	25.7314	38.9909

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 57:113)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 114:207)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 208:364)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 365:460)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 57:114)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 115:275)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 276:353)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 354:460)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 57:113)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 114:208)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 209:355)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 356:460)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 57:117)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 118:210)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 211:352)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 353:460)
17	X-RAY DIFFRACTION	17	(CHAIN F AND RESID 7:18)
18	X-RAY DIFFRACTION	18	(CHAIN G AND RESID 7:17)

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Protein , 1 types, 4 molecules ABCD

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TTLL6 unregistered ... , 2 types, 2 molecules FG

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Non-polymers , 5 types, 424 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi