+Open data
-Basic information
Entry | Database: PDB / ID: 2bqq | ||||||
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Title | X-ray Structure of the N-terminal Domain of Human Doublecortin | ||||||
Components | NEURONAL MIGRATION PROTEIN DOUBLECORTINDevelopment of the nervous system | ||||||
Keywords | TRANSFERASE / DCX DOMAIN / UBIQUITIN-LIKE FOLD / MICROTUBULE ASSOCIATED / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / retina development in camera-type eye / nervous system development / microtubule binding / microtubule / cytoskeleton ...axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / retina development in camera-type eye / nervous system development / microtubule binding / microtubule / cytoskeleton / neuron projection / intracellular signal transduction / protein kinase binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kim, M.H. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: The Dc-Module of Doublecortin: Dynamics, Domain Boundaries, and Functional Implications. Authors: Cierpicki, T. / Kim, M.H. / Cooper, D.R. / Derewenda, U. / Bushweller, J.H. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bqq.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bqq.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/2bqq ftp://data.pdbj.org/pub/pdb/validation_reports/bq/2bqq | HTTPS FTP |
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-Related structure data
Related structure data | 1mg4S 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
#1: Protein | Mass: 12944.309 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN RESIDUES 45-150 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGSTUNI1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43602 | ||
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#2: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | K134D, K135D MUTATIONS WERE TO AID CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.4 Details: 1.4 M NAH2PO4, 0.35 M K2HPO4, 0.6% PEG 150, SITTING DROP, pH 4.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 6002 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 2→2.28 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MG4 Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.956 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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