+Open data
-Basic information
Entry | Database: PDB / ID: 4qql | ||||||
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Title | Crystal structure of C1QL3 in P1 space group | ||||||
Components | Complement C1q-like protein 3 | ||||||
Keywords | PROTEIN BINDING / Jelly roll fold / C1q / Brain-specific angiogenesis inhibitor G-protein coupled receptor 3 / extracellular | ||||||
Function / homology | Function and homology information postsynaptic density assembly / collagen trimer / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse organization / synaptic cleft / hippocampal mossy fiber to CA3 synapse / glutamatergic synapse / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Ressl, S. / Brunger, A.T. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily. Authors: Ressl, S. / Vu, B.K. / Vivona, S. / Martinelli, D.C. / Sudhof, T.C. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qql.cif.gz | 644.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qql.ent.gz | 546.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/4qql ftp://data.pdbj.org/pub/pdb/validation_reports/qq/4qql | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15180.792 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql3, C1ql, Ctrp13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ESN4 #2: Chemical | ChemComp-MG / #3: 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: 2.28 Å3/Da / Density % sol: 46.03 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate, 20% Polyethylene glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→49.79 Å / Num. obs: 31044 / % possible obs: 65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Rmerge(I) obs: 0.06 / Rsym value: 0.085 / Net I/σ(I): 6.4 |
Reflection shell | Highest resolution: 2.39 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.285 / % possible all: 69.9 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→46.342 Å / SU ML: 0.29 / σ(F): 1.97 / Phase error: 31.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→46.342 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 27.7418 Å / Origin y: -1.5869 Å / Origin z: 34.7741 Å
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Refinement TLS group | Selection details: all |