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Yorodumi- PDB-3mdb: Crystal structure of the ternary complex of full length centaurin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mdb | ||||||
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Title | Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4 | ||||||
Components |
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Keywords | Transport Protein/Hydrolase Activator / KINESIN / GAP / GTPASE ACTIVATION / STRUCTURAL GENOMICS CONSORTIUM / SGC / CYTOSKELETON / MICROTUBULE / MOTOR PROTEIN / ZINC-FINGER / TRANSPORT PROTEIN-HYDROLASE ACTIVATOR COMPLEX / ATP-binding / Nucleotide-binding / Phosphoprotein / Metal-binding / Nucleus | ||||||
Function / homology | Function and homology information inositol 1,3,4,5 tetrakisphosphate binding / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / regulation of GTPase activity / phosphatidylinositol bisphosphate binding / regulation of axonogenesis / microtubule-based movement ...inositol 1,3,4,5 tetrakisphosphate binding / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / regulation of GTPase activity / phosphatidylinositol bisphosphate binding / regulation of axonogenesis / microtubule-based movement / phosphatidylinositol-3,4,5-trisphosphate binding / protein targeting / Nuclear signaling by ERBB4 / 14-3-3 protein binding / GTPase activator activity / T cell activation / microtubule binding / microtubule / cell surface receptor signaling pathway / axon / intracellular membrane-bounded organelle / protein kinase binding / signal transduction / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.952 Å | ||||||
Authors | Shen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4 Authors: Shen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mdb.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mdb.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mdb_validation.pdf.gz | 559.9 KB | Display | wwPDB validaton report |
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Full document | 3mdb_full_validation.pdf.gz | 568 KB | Display | |
Data in XML | 3mdb_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 3mdb_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/3mdb ftp://data.pdbj.org/pub/pdb/validation_reports/md/3mdb | HTTPS FTP |
-Related structure data
Related structure data | 3fm8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13969.805 Da / Num. of mol.: 2 / Fragment: Fha domain (UNP Residues 440 to 545) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF13B, GAKIN, KIAA0639 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9NQT8 #2: Protein | Mass: 45695.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAP1, CENTA1 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O75689 #3: Chemical | ChemComp-UNX / #4: Chemical | #5: Chemical | ChemComp-IP9 / ( | Sequence details | AUTHORS STATE THAT THEIR SEQUENCE MATCHES NCBI ENTRY NP_006860.1 GI:6806913 | |
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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: 2.66 Å3/Da / Density % sol: 58.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Sample buffer: 20mM HEPES, pH 7.30, 500mM NaCl, 1mM TCEP, 5% Glycerol. Protein complex was mixed with PIP3 in 1:1 molar ratio and acetone (5%). Reservoir solution: 0.8M lithium sulfate, 0.5M ...Details: Sample buffer: 20mM HEPES, pH 7.30, 500mM NaCl, 1mM TCEP, 5% Glycerol. Protein complex was mixed with PIP3 in 1:1 molar ratio and acetone (5%). Reservoir solution: 0.8M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Cryo-protectant: 2.0M lithium sulfate., vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR300 / Detector: CCD / Date: Oct 19, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→30 Å / Num. obs: 27800 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.139 / Χ2: 1.302 / Net I/σ(I): 6.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: nearly isomorphous coordinates of PDB entry 3FM8 Resolution: 2.952→29.437 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.205 / SU B: 18.738 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The programs PHENIX and COOT and the PRODRG and MOLPRPOBITY servers were also used during refinement.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.231 Å2
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Refinement step | Cycle: LAST / Resolution: 2.952→29.437 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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