+Open data
-Basic information
Entry | Database: PDB / ID: 6y4m | ||||||
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Title | Structure of Tubulin Tyrosine Ligase in Complex with Tb111 | ||||||
Components |
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Keywords | LIGASE / TTL / Tubulin / complex | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Gallus gallus (chicken) Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.34 Å | ||||||
Authors | Gavrilyuk, J. / Nocek, B. / Rigol, S. / Nicolaou, K.C. / Stoll, V. | ||||||
Citation | Journal: J.Org.Chem. / Year: 2021 Title: Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding ...Title: Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding Derived from X-ray Crystallographic Analysis. Authors: Nicolaou, K.C. / Pan, S. / Pulukuri, K.K. / Ye, Q. / Rigol, S. / Erande, R.D. / Vourloumis, D. / Nocek, B.P. / Munneke, S. / Lyssikatos, J. / Valdiosera, A. / Gu, C. / Lin, B. / Sarvaiaya, H. ...Authors: Nicolaou, K.C. / Pan, S. / Pulukuri, K.K. / Ye, Q. / Rigol, S. / Erande, R.D. / Vourloumis, D. / Nocek, B.P. / Munneke, S. / Lyssikatos, J. / Valdiosera, A. / Gu, C. / Lin, B. / Sarvaiaya, H. / Trinidad, J. / Sandoval, J. / Lee, C. / Hammond, M. / Aujay, M. / Taylor, N. / Pysz, M. / Purcell, J.W. / Gavrilyuk, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y4m.cif.gz | 911.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y4m.ent.gz | 749.3 KB | Display | PDB format |
PDBx/mmJSON format | 6y4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y4m_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6y4m_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6y4m_validation.xml.gz | 73.7 KB | Display | |
Data in CIF | 6y4m_validation.cif.gz | 99.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y4m ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y4m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _
NCS ensembles :
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-Components
-Protein , 4 types, 6 molecules ACBDEF
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4 #2: Protein | Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043 #4: Protein | | Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43 |
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-Non-polymers , 12 types, 50 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-GDP / | #9: Chemical | ChemComp-MES / | #10: Chemical | ChemComp-O9B / ( | #11: Chemical | ChemComp-O9H / [( | #12: Chemical | ChemComp-OH5 / ( | #13: Chemical | ChemComp-PGE / | #14: Chemical | ChemComp-VAL / | #15: Chemical | ChemComp-ACP / | #16: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.03 M calcium chloride, 0.03 M magnesium chloride, 0.10 M MES pH 6.50, 3.20% w/v PEG 4000, 5.00% w/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.34→30 Å / Num. obs: 43404 / % possible obs: 99.5 % / Redundancy: 4.2 % / CC1/2: 0.975 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.114 / Rrim(I) all: 0.245 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 3.34→3.52 Å / Rmerge(I) obs: 0.683 / Num. unique obs: 6256 / CC1/2: 0.617 / Rpim(I) all: 0.353 / Rrim(I) all: 0.772 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.34→29.9 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.902 / SU B: 65.786 / SU ML: 0.454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.524 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 184.33 Å2 / Biso mean: 82.208 Å2 / Biso min: 2.4 Å2
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Refinement step | Cycle: final / Resolution: 3.34→29.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.34→3.425 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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