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- PDB-6vzq: Engineered TTLL6 mutant bound to alpha-elongation analog -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6vzq
TitleEngineered TTLL6 mutant bound to alpha-elongation analog
ComponentsTubulin polyglutamylase TTLL6
KeywordsLIGASE / Protein engineering / TTLL6 / amino acid ligase / glutamylation
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 ...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 / tubulin binding / ciliary basal body / cilium / microtubule cytoskeleton organization / microtubule / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-RZP / Chem-RZY / Tubulin polyglutamylase TTLL6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsMahalingan, K.K. / Keenen, E.K. / Strickland, E.K. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.
Funding support United States, 2items
OrganizationGrant numberCountry
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 NS 003122 United States
CitationJournal: 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
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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 1.2Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin polyglutamylase TTLL6
B: Tubulin polyglutamylase TTLL6
C: Tubulin polyglutamylase TTLL6
D: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,61738
Polymers213,3824
Non-polymers5,23634
Water1,72996
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A: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1965
Polymers53,3451
Non-polymers8514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,89912
Polymers53,3451
Non-polymers1,55411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3476
Polymers53,3451
Non-polymers1,0015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,17515
Polymers53,3451
Non-polymers1,83014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.038, 109.491, 171.700
Angle α, β, γ (deg.)90.000, 90.014, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 57 through 64 or (resid 65...A57 - 331
121(chain 'A' and (resid 57 through 64 or (resid 65...A333 - 350
131(chain 'A' and (resid 57 through 64 or (resid 65...A352 - 410
141(chain 'A' and (resid 57 through 64 or (resid 65...A418 - 460
151(chain 'A' and (resid 57 through 64 or (resid 65...A501
211(chain 'B' and ((resid 57 through 60 and (name N...B57 - 331
221(chain 'B' and ((resid 57 through 60 and (name N...B333 - 350
231(chain 'B' and ((resid 57 through 60 and (name N...B352 - 410
241(chain 'B' and ((resid 57 through 60 and (name N...B418 - 460
251(chain 'B' and ((resid 57 through 60 and (name N...B501
311(chain 'C' and ((resid 57 through 60 and (name N...C57 - 331
321(chain 'C' and ((resid 57 through 60 and (name N...C333 - 350
331(chain 'C' and ((resid 57 through 60 and (name N...C352 - 410
341(chain 'C' and ((resid 57 through 60 and (name N...C418 - 460
351(chain 'C' and ((resid 57 through 60 and (name N...C501
411(chain 'D' and ((resid 57 through 60 and (name N...D57 - 331
421(chain 'D' and ((resid 57 through 60 and (name N...D333 - 350
431(chain 'D' and ((resid 57 through 60 and (name N...D352 - 410
441(chain 'D' and ((resid 57 through 60 and (name N...D418 - 460
451(chain 'D' and ((resid 57 through 60 and (name N...D501

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Components

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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: C179A, Q180R, 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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Non-polymers , 6 types, 130 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-RZY / (2~{S})-2-[[[(1~{S})-1-acetamidoethyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid


Mass: 375.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19NO10P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-RZP / (2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid


Mass: 433.242 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H21NO12P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM Sodium Citrate, pH 6.2, 200 mM MgCl2, 12% Peg 20000
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.08→46.16 Å / Num. obs: 101188 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 57.3 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06054 / Rpim(I) all: 0.0605 / Rrim(I) all: 0.08561 / Net I/σ(I): 7.16
Reflection shellResolution: 3.08→3.194 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2512 / Mean I/σ(I) obs: 2.65 / Num. unique obs: 9901 / CC1/2: 0.918 / CC star: 0.978 / Rpim(I) all: 0.251 / Rrim(I) all: 0.3552 / % possible all: 98.36

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLR

4ylr


Resolution: 3.08→46.16 Å / SU ML: 0.3877 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.3173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2593 5094 5.14 %
Rwork0.2259 94093 -
obs0.2277 99187 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.88 Å2
Refinement stepCycle: LAST / Resolution: 3.08→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12026 0 328 96 12450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001812646
X-RAY DIFFRACTIONf_angle_d0.538717215
X-RAY DIFFRACTIONf_chiral_restr0.03871893
X-RAY DIFFRACTIONf_plane_restr0.00252191
X-RAY DIFFRACTIONf_dihedral_angle_d14.12697386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.120.37851620.34072967X-RAY DIFFRACTION92.46
3.12-3.160.33391860.29273092X-RAY DIFFRACTION99.21
3.16-3.190.34792100.26163169X-RAY DIFFRACTION99.12
3.19-3.230.26061920.24693153X-RAY DIFFRACTION98.79
3.23-3.280.33271890.24193075X-RAY DIFFRACTION99.03
3.28-3.320.2291940.22073083X-RAY DIFFRACTION98.08
3.32-3.370.29261870.24373121X-RAY DIFFRACTION97.81
3.37-3.420.37341630.23623175X-RAY DIFFRACTION98.58
3.42-3.470.31521310.25673129X-RAY DIFFRACTION98.16
3.47-3.530.28141660.24423098X-RAY DIFFRACTION97.64
3.53-3.590.28181500.2293161X-RAY DIFFRACTION99.31
3.59-3.660.25681340.23013172X-RAY DIFFRACTION98.8
3.66-3.730.27541880.22523176X-RAY DIFFRACTION98.94
3.73-3.80.30911210.20713227X-RAY DIFFRACTION98.91
3.8-3.890.2931580.21733137X-RAY DIFFRACTION99.04
3.89-3.980.25931670.21623147X-RAY DIFFRACTION98.93
3.98-4.080.21851340.21143193X-RAY DIFFRACTION98.99
4.08-4.190.21361580.19953165X-RAY DIFFRACTION98.96
4.19-4.310.25141580.21233148X-RAY DIFFRACTION98.92
4.31-4.450.25111700.19613161X-RAY DIFFRACTION98.2
4.45-4.610.21571610.19943107X-RAY DIFFRACTION98.76
4.61-4.790.23972000.19683150X-RAY DIFFRACTION99.23
4.79-5.010.27911840.21213179X-RAY DIFFRACTION99.76
5.01-5.270.28211890.22853156X-RAY DIFFRACTION99.73
5.27-5.60.32131840.2463121X-RAY DIFFRACTION99.34
5.6-6.030.29622000.25243159X-RAY DIFFRACTION98.71
6.03-6.640.28981300.24373144X-RAY DIFFRACTION97.91
6.64-7.60.23311770.24983120X-RAY DIFFRACTION98.8
7.6-9.560.17961710.20343177X-RAY DIFFRACTION99.79
9.56-46.160.17671800.21883031X-RAY DIFFRACTION95.4
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.90640556703E-50.00476728203290.001897251813930.003704172798140.0006839216742290.00920759475772-0.00569615145753-0.00254345180415-0.01488404600040.00706939752616-0.0259919651659-0.02480069992770.0220693410255-0.0259803586022-4.70509315943E-80.979382409194-0.127721861487-0.004618970239350.772428225234-0.07984630049520.38193434237938.607023176425.015730558420.2454064123
2-0.00426413633190.0241706033312-0.001673309239370.0159917959187-0.01226243316060.02412587700810.0959408335044-0.0254834370779-0.08099969696970.0133967697138-0.002866381829950.104766087097-0.09708078024480.06447721081693.78521860765E-90.990463621285-0.07907078405840.1775418145190.703077189495-0.10744446902-0.048017676233312.384963640913.1306568710.4541707011
30.0146275890686-0.000495389421619-0.001879771248890.0262354106919-0.00735460893040.00522163614477-0.005172156714790.04645082667290.03633507276170.0665161791443-0.0250657844934-0.004687061042470.007525843750980.005253360907241.50242736535E-81.0008783713-0.01435813502770.1641177727630.808808933715-0.05374116421810.38595442288318.133109178928.42804882812.4302170628
4-0.0005764869141850.01263179977890.002949321010530.0221198480306-0.01485317460730.009275628916310.02452125329690.08005597143330.06576841407720.0609777115836-0.07123484660.0247701333157-0.009596476282970.00165314906854-9.92603064366E-100.983435528353-0.09333947530730.09707289135960.748680415993-0.1246661961170.24825918733923.373892459431.956117199518.2955502694
50.004574600780480.03938158702690.002394402295890.038721465480.0007484890044640.0283917771482-0.1551716703450.269621639199-0.00876565314375-0.4313980548610.0778364261831-0.0512042087516-0.176346008115-0.09441734737961.81779357168E-9-1.304580456160.46359673110.120878274479-0.189087730627-0.09565681303040.11846812284816.3319147329-6.7372721333466.9948047169
60.03260022343170.01825560785650.03268775364260.01892606379580.01905177657580.0003165315291580.073540174468-0.0939915909268-0.0413122456014-0.0383280670253-0.07481871201480.09343634979330.05189792320940.0755249391813-1.65351920494E-8-0.654255005468-0.5310344024890.0630666740431-0.1845327928480.01256511886060.36563204715920.5943656438-4.6421810594983.1523973897
70.03205535947250.01545947399120.005584876771340.0104128690710.0117671390316-0.00219794114274-0.00144361554756-0.04734446538170.0979263391292-0.307251037211-0.0479061622332-0.0324043461713-0.0285754771645-0.07973464637894.03181031202E-9-0.4045125313720.0540249346875-0.0415675659020.161106951916-0.02885732660190.50587238821218.42308650753.7749172999672.4954008059
8-0.00185130998256-0.00377553847192-0.009857603773220.00958112077687-0.030823657584-0.00516675436466-0.0118375815247-0.001713856329650.00302736910608-0.08987569824920.002867931731890.0319254711718-0.1494331846680.0297684481223-3.69104070532E-80.337735522804-0.0369127816422-0.01831423281080.2037880526730.2044325645230.45899404905612.754124770815.811197751858.6307579192
90.002446779188370.00241380009061-0.001269337954950.002809225285680.0002996130329850.00816705523115-0.0204209253504-0.01882448254740.005914050198810.011978775048-0.01915266989680.0466302057808-0.01734881384490.00708861703288-1.3110527087E-80.869130559931-0.002912878136720.03050602829560.9043977097230.0900377130940.35281670448-1.55265590916-22.51184189220.5449130869
10-0.0006502137620830.0196077674025-0.005419729747330.01172870819690.01284303660360.01767142735250.0365399547193-0.05579668884790.08802211255930.00313011954011-0.0137362155411-0.07952349774980.0569566243407-0.0407629168701-7.80246194342E-100.8987551689690.008107753151020.001795803892030.751613101775-0.0471906352977-0.014313862630824.9198283287-10.596588089810.9614104981
110.0182940789944-0.007822861167790.004500270199090.01854275753120.002327004882820.005833023099680.04391243851610.00179277181045-0.02325074229020.0227127639067-0.0288700366215-0.00369655357479-0.002218701688290.01711131988681.60595223875E-90.8844808138090.14522994206-0.07015072216580.876023508666-0.06253399565890.41157202527421.5519516949-25.12987222129.95245047273
12-0.0058842105503-0.00892021486558-0.002569203251260.00747834255939-0.001752559919710.00634665410647-0.00578027460374-0.0401728902039-0.08319302076910.01909339461140.02254612867040.024114278997-0.0439178112812-0.000170391565885-3.82352196673E-90.8606649919410.002090551014480.05241250482610.763459929120.06523340212910.26844047399913.818818374-29.564759518820.575104656
13-0.0105204212809-0.00941334694130.00267842891998-0.001799709969770.0003130788904520.00316267431715-0.0356254132380.0765984325371-0.00685625844649-0.0997180171772-0.0381645981745-0.04832876068920.01038471672210.04143109994099.44622669374E-9-0.06174870211140.3253474501980.156502765502-0.0839041750427-0.1702819526170.12194877859639.0384375771-45.420291163165.5528805587
140.0028837433524-0.001876502582270.03025568567630.00602133035287-0.0114315008045-0.01100936975770.0001676671825360.09850089120420.00570850509195-0.140785306518-0.04487840981690.02295268133970.0340495828975-0.1352505084097.23253620227E-9-0.834972318460.497388024555-0.364079419377-0.1841189504390.1210738694410.2459875280518.34941566223-29.685662096968.6376681901
150.074418335593-0.00517017685941-0.01063921918890.0069320178947-0.0526554836233-0.004628739180850.146619980584-0.169581572371-0.0567203478297-0.49408468521-0.172267408801-0.01117612895090.1505435195860.164043024647-4.727936986E-9-0.901368097280.054405811373-0.1597367808870.21250471141-0.004927777743330.38259946836216.8322559601-41.94886748178.2693025111
16-0.002379097900890.0170452911663-0.03723338212930.006496832478540.047451300228-0.0394559843955-0.02931597015120.0359788005276-0.113346233713-0.461543782751-0.117885049205-0.05029319992030.3771325779540.1779007813092.37245982315E-9-0.5781279660190.227056358852-0.0704865409338-0.651687431933-0.2381426954490.32288842155723.3289621745-52.216862895666.3498382857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 57:116)
2X-RAY DIFFRACTION2(chain A and resid 117:275)
3X-RAY DIFFRACTION3(chain A and resid 276:341)
4X-RAY DIFFRACTION4(chain A and resid 342:460)
5X-RAY DIFFRACTION5(chain B and resid 57:197)
6X-RAY DIFFRACTION6(chain B and resid 198:291)
7X-RAY DIFFRACTION7(chain B and resid 292:384)
8X-RAY DIFFRACTION8(chain B and resid 385:460)
9X-RAY DIFFRACTION9(chain C and resid 57:114)
10X-RAY DIFFRACTION10(chain C and resid 115:275)
11X-RAY DIFFRACTION11(chain C and resid 276:330)
12X-RAY DIFFRACTION12(chain C and resid 331:460)
13X-RAY DIFFRACTION13(chain D and resid 57:115)
14X-RAY DIFFRACTION14(chain D and resid 116:197)
15X-RAY DIFFRACTION15(chain D and resid 198:339)
16X-RAY DIFFRACTION16(chain D and resid 340:460)

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