+Open data
-Basic information
Entry | Database: PDB / ID: 3coo | ||||||
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Title | The crystal structure of Reelin-N domain of F-spondin | ||||||
Components | Spondin-1 | ||||||
Keywords | CELL ADHESION / F-spondin / reelin-N domain / Extracellular matrix / Glycoprotein / Secreted | ||||||
Function / homology | Function and homology information positive regulation of amyloid precursor protein catabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / positive regulation of protein processing / extracellular matrix structural constituent / LBD domain binding / negative regulation of amyloid-beta formation / extracellular matrix / protein processing / cell adhesion ...positive regulation of amyloid precursor protein catabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / positive regulation of protein processing / extracellular matrix structural constituent / LBD domain binding / negative regulation of amyloid-beta formation / extracellular matrix / protein processing / cell adhesion / endoplasmic reticulum lumen / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Tan, K. / Lawler, J. / Wang, J.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The crystal structure of the heparin-binding reelin-N domain of f-spondin. Authors: Tan, K. / Duquette, M. / Liu, J.H. / Lawler, J. / Wang, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3coo.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3coo.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 3coo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/3coo ftp://data.pdbj.org/pub/pdb/validation_reports/co/3coo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | Domain is a monomer in solution. Chains A and B may form a low affinity and fast off rate dimer. |
-Components
#1: Protein | Mass: 20498.869 Da / Num. of mol.: 2 / Fragment: Reelin-N domain (UNP residues 29-194) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Homo sapiens / Plasmid: pMT/BiP V5-HisA / Cell line (production host): S2 cell / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9HCB6 #2: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M Ammonium sulfate, 30% (W/V) PEG 4000, 0.1M Sodium Citrate tribasic dehydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2005 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 26814 / Num. obs: 26814 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 36.58 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4 / Num. unique all: 2485 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→40.06 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.458 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.153 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.928 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.05 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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