+Open data
-Basic information
Entry | Database: PDB / ID: 9etn | ||||||
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Title | Crystal structure of murine CRTAC1 | ||||||
Components | Cartilage acidic protein 1 | ||||||
Keywords | SIGNALING PROTEIN / beta-propeller / potassium binding / calcium binding | ||||||
Function / homology | Function and homology information olfactory bulb development / axonal fasciculation / regulation of synapse assembly / growth cone / postsynaptic density / glutamatergic synapse / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 Å | ||||||
Authors | Beugelink, J.W. / Hof, H. / Janssen, B.J.C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2024 Title: CRTAC1 has a Compact beta-propeller-TTR Core Stabilized by Potassium Ions. Authors: Beugelink, J.W. / Hof, H. / Janssen, B.J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9etn.cif.gz | 262.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9etn.ent.gz | 193.4 KB | Display | PDB format |
PDBx/mmJSON format | 9etn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9etn_validation.pdf.gz | 818.1 KB | Display | wwPDB validaton report |
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Full document | 9etn_full_validation.pdf.gz | 818.5 KB | Display | |
Data in XML | 9etn_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 9etn_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/9etn ftp://data.pdbj.org/pub/pdb/validation_reports/et/9etn | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 64157.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crtac1, Aspic1, Cep68 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8R555 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 324 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.2 Å3/Da / Density % sol: 61.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium-malonate pH 5.0, 12% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6702 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6702 Å / Relative weight: 1 |
Reflection | Resolution: 1.582→81.707 Å / Num. obs: 54952 / % possible obs: 86.5 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.042 / Rrim(I) all: 0.099 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.582→1.786 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.777 / Num. unique obs: 2748 / CC1/2: 0.667 / Rpim(I) all: 0.409 / Rrim(I) all: 0.885 / % possible all: 67.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.584→81.707 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.149 / Average fsc free: 0.9742 / Average fsc work: 0.9849 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.117 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.695 Å2
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Refinement step | Cycle: LAST / Resolution: 1.584→81.707 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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