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- PDB-3tig: Tubulin tyrosine ligase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3tig
TitleTubulin tyrosine ligase
ComponentsTtl protein
KeywordsLIGASE / ATP-grasp / tubulin
Function / homology
Function and homology information


tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / protein modification process / spindle microtubule / microtubule cytoskeleton organization / ATP binding / metal ion binding
Similarity search - Function
Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich ...Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tubulin--tyrosine ligase / Tubulin--tyrosine ligase
Similarity search - Component
Biological speciesXenopus tropicalis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsRoll-Mecak, A. / Szyk, A. / Deaconescu, A. / Piszczek, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Tubulin tyrosine ligase structure reveals adaptation of an ancient fold to bind and modify tubulin.
Authors: Szyk, A. / Deaconescu, A.M. / Piszczek, G. / Roll-Mecak, A.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ttl protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7883
Polymers43,7401
Non-polymers492
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.570, 76.220, 44.240
Angle α, β, γ (deg.)90.00, 90.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ttl protein


Mass: 43739.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (Silurana) tropicalis (tropical clawed frog)
Gene: ttl / Production host: Escherichia coli (E. coli) / References: UniProt: A9ULH4, UniProt: F6Z895*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes 7.5, 8% Peg8000, 8% ethylene glycol, 0.05M Magnesium Chloride, 10mM Barium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781, 0.9806, 0.9637
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07811
20.98061
30.96371
ReflectionResolution: 2.5→50 Å / Num. all: 13383 / Num. obs: 13383 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 41.4 Å2 / Rsym value: 0.061 / Net I/σ(I): 52
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 5 / Rsym value: 0.333 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BOSdata collection
SHARPphasing
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→44.24 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 148994.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1308 10.1 %RANDOM
Rwork0.25 ---
obs0.25 12946 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.6522 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 73.4 Å2
Baniso -1Baniso -2Baniso -3
1--23.74 Å20 Å213.85 Å2
2--11.61 Å20 Å2
3---12.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 2 37 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.912.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 185 9.5 %
Rwork0.331 1759 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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