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Yorodumi- PDB-8ovq: Crystal structure of Geodia cydonium sponge adhesion molecule lon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ovq | |||||||||
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Title | Crystal structure of Geodia cydonium sponge adhesion molecule long form (SAML). | |||||||||
Components | Cell recognition molecule, long form | |||||||||
Keywords | IMMUNE SYSTEM / Ig-like / porifera / evolution | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Geodia cydonium (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||
Authors | Lopez-Sagaseta, J. / Urdiciain, A. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Geodia cydonium sponge adhesion molecule long form (SAML). Authors: Lopez-Sagaseta, J. / Urdiciain, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ovq.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ovq.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ovq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ovq_validation.pdf.gz | 470.3 KB | Display | wwPDB validaton report |
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Full document | 8ovq_full_validation.pdf.gz | 471.7 KB | Display | |
Data in XML | 8ovq_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 8ovq_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/8ovq ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ovq | 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
#1: Protein | Mass: 24394.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Remaining N-terminal GP motif from 3C site / Source: (gene. exp.) Geodia cydonium (invertebrata) / Gene: crml / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U965 | ||||||
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#2: Sugar | ChemComp-NAG / | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG4000, 0.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2022 |
Radiation | Monochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→77.8 Å / Num. obs: 27255 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.056 / Rrim(I) all: 0.088 / Χ2: 1.02 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1358 / CC1/2: 0.576 / Χ2: 1.03 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→38.931 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.147 / SU B: 4.543 / SU ML: 0.067 / Average fsc free: 0.968 / Average fsc work: 0.9808 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.086 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: 27.475 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→38.931 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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