PDB-5vlq: Structure of the TTLL3 Glycylase

ID or keywords:

Entry

Database: PDB / ID: 5vlq

Title

Structure of the TTLL3 Glycylase

Components

LOC100158544 protein

Keywords

LIGASE / glycylase / tubulin / TTLL3 / microtubule

Function / homology

Function and homology information

protein polyglycylation / protein-glycine ligase activity, initiating / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / motile cilium / microtubule / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Xenopus tropicalis (tropical clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.285 Å

Authors

Garnham, C.P. / Yu, I. / Li, Y. / Roll-Mecak, A.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structure of tubulin tyrosine ligase-like 3 reveals essential architectural elements unique to tubulin monoglycylases.
Authors: Garnham, C.P. / Yu, I. / Li, Y. / Roll-Mecak, A.

History

Deposition	Apr 25, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 31, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 21, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 5, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5vlq.cif.gz	464.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5vlq.ent.gz	382.6 KB	Display	PDB format
PDBx/mmJSON format	5vlq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5vlq_validation.pdf.gz	1016.4 KB	Display	wwPDB validaton report
Full document	5vlq_full_validation.pdf.gz	1020.5 KB	Display
Data in XML	5vlq_validation.xml.gz	31.1 KB	Display
Data in CIF	5vlq_validation.cif.gz	43.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vl/5vlq ftp://data.pdbj.org/pub/pdb/validation_reports/vl/5vlq	HTTPS FTP

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Related structure data

Similar structure data	3e0j-1 5nf3-d 1iil-3 6wiq-1 5f7l-1 5f7l-2 4k7k-2 4k7k-1 2fvu-d 6a93-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#175 - Jul 2014 Microtubules similarity (2) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#175 - Jul 2014
Microtubules
similarity (2)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: LOC100158544 protein

B: LOC100158544 protein

hetero molecules

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

1

A: LOC100158544 protein

hetero molecules

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

2

B: LOC100158544 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.625, 192.241, 60.743
Angle α, β, γ (deg.)	90.00, 114.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	LOC100158544 protein Mass: 67760.281 Da / Num. of mol.: 2 / Fragment: UNP residues 6-569 / Mutation: E520Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: LOC100158544 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: B2GUB3
#2: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	The gamma phosphate group of the AMPPNP molecule in the active site was disordered, and hence was ...The gamma phosphate group of the AMPPNP molecule in the active site was disordered, and hence was not modelled by the authors

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.23 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris-HCl (pH 8), 20% PEG 3350, 200 mM LiSO4.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9777 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Feb 24, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9777 Å / Relative weight: 1
Reflection	Resolution: 2.28→48.89 Å / Num. obs: 53787 / % possible obs: 97.4 % / Redundancy: 3.7 % / R_sym value: 0.077 / Net I/σ(I): 16.4
Reflection shell	Resolution: 2.28→2.32 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.5 / R_sym value: 0.508 / % possible all: 75.6

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.9_1692	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.285→48.493 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2327	5343	9.93 %
R_work	0.2064	-	-
obs	0.209	53787	97.34 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.285→48.493 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6190	0	64	253	6507

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6412
X-RAY DIFFRACTION	f_angle_d	0.63	8739
X-RAY DIFFRACTION	f_dihedral_angle_d	11.59	2175
X-RAY DIFFRACTION	f_chiral_restr	0.029	971
X-RAY DIFFRACTION	f_plane_restr	0.002	1100

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 (%)
2.285-2.3109	0.2762	143	0.2599	1199	X-RAY DIFFRACTION	72
2.3109-2.3381	0.2911	162	0.2749	1346	X-RAY DIFFRACTION	82
2.3381-2.3666	0.3157	147	0.2663	1472	X-RAY DIFFRACTION	90
2.3666-2.3966	0.2774	163	0.2682	1555	X-RAY DIFFRACTION	93
2.3966-2.4281	0.3035	166	0.2708	1557	X-RAY DIFFRACTION	93
2.4281-2.4614	0.2732	197	0.2463	1547	X-RAY DIFFRACTION	96
2.4614-2.4965	0.305	181	0.2469	1647	X-RAY DIFFRACTION	99
2.4965-2.5338	0.2796	188	0.2519	1635	X-RAY DIFFRACTION	99
2.5338-2.5734	0.2734	185	0.2487	1643	X-RAY DIFFRACTION	100
2.5734-2.6156	0.2884	174	0.2438	1653	X-RAY DIFFRACTION	100
2.6156-2.6607	0.2748	162	0.2395	1668	X-RAY DIFFRACTION	100
2.6607-2.7091	0.2457	216	0.2301	1634	X-RAY DIFFRACTION	100
2.7091-2.7612	0.275	181	0.2262	1663	X-RAY DIFFRACTION	100
2.7612-2.8175	0.2548	185	0.2311	1647	X-RAY DIFFRACTION	100
2.8175-2.8788	0.2431	170	0.2327	1652	X-RAY DIFFRACTION	100
2.8788-2.9457	0.2339	178	0.2118	1670	X-RAY DIFFRACTION	100
2.9457-3.0194	0.2712	148	0.2115	1671	X-RAY DIFFRACTION	100
3.0194-3.101	0.2252	195	0.2117	1677	X-RAY DIFFRACTION	100
3.101-3.1922	0.2358	187	0.2149	1640	X-RAY DIFFRACTION	100
3.1922-3.2953	0.2253	176	0.217	1647	X-RAY DIFFRACTION	100
3.2953-3.413	0.2543	185	0.2105	1672	X-RAY DIFFRACTION	100
3.413-3.5496	0.2335	169	0.2068	1656	X-RAY DIFFRACTION	100
3.5496-3.7111	0.2069	198	0.1977	1649	X-RAY DIFFRACTION	100
3.7111-3.9067	0.2118	177	0.1797	1662	X-RAY DIFFRACTION	100
3.9067-4.1513	0.2053	187	0.1696	1646	X-RAY DIFFRACTION	100
4.1513-4.4717	0.1736	190	0.1589	1663	X-RAY DIFFRACTION	100
4.4717-4.9213	0.1682	189	0.1639	1668	X-RAY DIFFRACTION	100
4.9213-5.6325	0.2007	182	0.1882	1652	X-RAY DIFFRACTION	100
5.6325-7.0928	0.2835	178	0.2182	1675	X-RAY DIFFRACTION	100
7.0928-48.5039	0.2451	184	0.209	1678	X-RAY DIFFRACTION	99

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	1.4415	-1.2304	-3.4276	2.0833	2.6353	8.064	-0.0841	-0.1156	0.0558	0.1102	0.1015	0.1066	0.1408	-0.1579	-0.0229	0.219	0.0205	-0.048	0.306	0.0318	0.2623	-32.1501	-0.0018	22.6944
2	1.0048	-1.5071	-0.8324	6.3348	2.5866	1.7361	-0.1234	0.1177	-0.3534	-0.1127	-0.081	0.2643	0.3591	0.0221	0.1432	0.4538	0.0615	0.0198	0.3206	-0.0204	0.3735	-17.2327	-28.1639	0.2034
3	2.7252	0.5711	-2.6559	1.9497	-0.7931	2.6065	-0.1347	0.7185	-0.1335	0.1818	0.2205	0.371	0.0995	-0.8682	-0.0985	0.3232	-0.0577	-0.0793	0.661	0.1005	0.4399	-54.1732	0.7312	-13.1178
4	5.3151	2.4391	-0.9492	3.181	-0.8418	2.6096	0.1698	0.0827	0.0361	-0.0214	0.0672	0.3004	0.0878	-0.3376	-0.2223	0.2635	0.0357	-0.0628	0.2513	0.0369	0.2178	-34.0021	5.3767	-8.2184
5	3.1695	4.5354	1.7514	7.7285	2.2154	2.0284	0.2357	-0.2557	0.1311	0.4921	-0.1795	-0.6165	-0.4185	0.3066	-0.0534	0.5555	-0.2083	0.0177	0.4894	-0.0812	0.6019	-5.927	40.0668	-6.4848
6	2.7338	2.4235	1.267	2.1168	0.8889	0.8757	0.2202	-0.0641	0.6196	0.2192	-0.046	0.121	-0.4539	0.1427	-0.1179	0.6525	-0.1922	0.1388	0.369	-0.0954	0.548	-17.1495	36.394	-10.3671
7	2.635	-0.762	-0.6385	7.474	-0.8488	2.2297	0.2097	0.0192	0.56	-0.3728	0.0924	0.3315	-0.3662	-0.0584	-0.2253	0.3262	-0.039	-0.0159	0.2683	0.0202	0.3155	-30.2519	24.3696	-18.2443
8	4.9826	1.9234	-0.3444	4.2956	-0.5185	1.3262	-0.0238	0.2481	0.489	-0.3319	0.1613	0.6758	-0.0898	-0.1936	-0.1291	0.3719	0.0114	-0.0614	0.3127	0.0934	0.2786	-35.2365	17.6589	-20.2679

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 127 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 128 through 569 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 4 through 99 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 100 through 158 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 159 through 300 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 301 through 396 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 397 through 510 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 511 through 569 )

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