+Open data
-Basic information
Entry | Database: PDB / ID: 6th4 | ||||||
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Title | Tubulin-inhibitor complex | ||||||
Components |
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Keywords | CELL CYCLE / cytoskeleton / cell division / intracellular transport / TRANSPORT PROTEIN / MICROTUBULE | ||||||
Function / homology | Function and homology information microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / neuron projection development / growth cone / neuron projection / Golgi apparatus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.121 Å | ||||||
Authors | Varela, P.F. / Gigant, B. | ||||||
Citation | Journal: Acs Omega / Year: 2022 Title: B-nor-methylene Colchicinoid PT-100 Selectively Induces Apoptosis in Multidrug-Resistant Human Cancer Cells via an Intrinsic Pathway in a Caspase-Independent Manner Authors: Stein, A. / Hilken nee Thomopoulou, P. / Frias, C. / Hopff, S.M. / Varela, P. / Wilke, N. / Mariappan, A. / Neudorfl, J.M. / Fedorov, A.Y. / Gopalakrishnan, J. / Gigant, B. / Prokop, A. / Schmalz, H.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6th4.cif.gz | 756.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6th4.ent.gz | 627.2 KB | Display | PDB format |
PDBx/mmJSON format | 6th4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6th4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6th4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6th4_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 6th4_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6th4 ftp://data.pdbj.org/pub/pdb/validation_reports/th/6th4 | HTTPS FTP |
-Related structure data
Related structure data | 3rycS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 5 molecules ACBDE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) #3: Protein | | Mass: 16745.975 Da / Num. of mol.: 1 / Mutation: C14A, F20W 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 |
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-Non-polymers , 6 types, 132 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: 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: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG, LiSO4, PIPES BUFFER, pH 6.80 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→126 Å / Num. obs: 62794 / % possible obs: 94 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.12→2.42 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3141 / CC1/2: 0.627 / Rrim(I) all: 1.151 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RYC Resolution: 2.121→126 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 1.107 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.974 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.29
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Displacement parameters | Biso mean: 66.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.121→126 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.121→2.316 Å
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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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