+Open data
-Basic information
Entry | Database: PDB / ID: 4f61 | ||||||
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Title | Tubulin:Stathmin-like domain complex | ||||||
Components |
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Keywords | CELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE / MICROTUBULE / RB3 / STATHMIN TUBULIN | ||||||
Function / homology | Function and homology information axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / recycling endosome / structural constituent of cytoskeleton / cerebral cortex development / memory / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / mitotic cell cycle / gene expression / neuron apoptotic process / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Artificial gene (others) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.17 Å | ||||||
Authors | Gigant, B. / Mignot, I. / Knossow, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Design and characterization of modular scaffolds for tubulin assembly. Authors: Mignot, I. / Pecqueur, L. / Dorleans, A. / Karuppasamy, M. / Ravelli, R.B. / Dreier, B. / Pluckthun, A. / Knossow, M. / Gigant, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f61.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4f61.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 4f61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f61_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4f61_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 4f61_validation.xml.gz | 71.3 KB | Display | |
Data in CIF | 4f61_validation.cif.gz | 108.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/4f61 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f61 | HTTPS FTP |
-Related structure data
Related structure data | 4f6rC 3rycS C: citing same article (ref.) 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, 9 molecules ACEGBDFHI
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWZ0 #2: Protein | Mass: 49983.824 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWY9 #3: Protein | | Mass: 28782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Artificial gene (others) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Non-polymers , 3 types, 12 molecules
#4: Chemical | ChemComp-GTP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-GDP / |
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-Details
Sequence details | AUTHOR STATES THAT THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE ...AUTHOR STATES THAT THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT |
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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: 3.16 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG, NACL, PIPES BUFFER, PH 6.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 4.17→50 Å / Num. all: 40900 / Num. obs: 40336 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 125.69 Å2 / Rsym value: 0.112 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 4.17→4.28 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.65 / Rsym value: 0.876 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RYC Resolution: 4.17→49.04 Å / Cor.coef. Fo:Fc: 0.8202 / Cor.coef. Fo:Fc free: 0.8021 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 182.8 Å2
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Refine analyze | Luzzati coordinate error obs: 1.417 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.17→49.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.17→4.28 Å / 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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