+Open data
-Basic information
Entry | Database: PDB / ID: 3qh9 | ||||||
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Title | Human Liprin-beta2 Coiled-Coil | ||||||
Components | Liprin-beta-2 | ||||||
Keywords | STRUCTURAL PROTEIN / coiled-coil / dimerization | ||||||
Function / homology | Function and homology information Receptor-type tyrosine-protein phosphatases / neuromuscular junction development / presynaptic active zone / synapse organization / extracellular space / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Stafford, R.L. / Tang, M. / Phillips, M.L. / Bowie, J.U. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Crystal structure of the central coiled-coil domain from human liprin-beta2 Authors: Stafford, R.L. / Tang, M.Y. / Sawaya, M.R. / Phillips, M.L. / Bowie, J.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qh9.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qh9.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qh9_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 3qh9_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 3qh9_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 3qh9_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/3qh9 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qh9 | HTTPS FTP |
-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
#1: Protein | Mass: 9742.104 Da / Num. of mol.: 1 / Fragment: UNP Residues 185-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPFIBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q8ND30 |
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#2: Chemical | ChemComp-IOD / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-NH4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 190 mM ammonium iodide, 23% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.4938 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4938 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→81.38 Å / Num. all: 5774 / Num. obs: 5774 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→81.38 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.827 / WRfactor Rfree: 0.3199 / WRfactor Rwork: 0.2887 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.7778 / SU B: 10.226 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2572 / SU Rfree: 0.2294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.69 Å2 / Biso mean: 37.226 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→81.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.062 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 2.553 Å / Origin y: 19.803 Å / Origin z: 7.429 Å
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