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Yorodumi- PDB-8sip: Structure of a mouse IgG antibody fragment that binds Inosine, an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sip | ||||||
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Title | Structure of a mouse IgG antibody fragment that binds Inosine, an RNA modification | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IgG Fab / Inosine / RNA binding protein / modified RNA / small molecule ligand | ||||||
Function / homology | INOSINE Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Aoki, S.T. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of a mouse IgG antibody fragment that binds Inosine, an RNA modification Authors: Aoki, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sip.cif.gz | 208.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sip.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 8sip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sip_validation.pdf.gz | 765.6 KB | Display | wwPDB validaton report |
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Full document | 8sip_full_validation.pdf.gz | 770.9 KB | Display | |
Data in XML | 8sip_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 8sip_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/8sip ftp://data.pdbj.org/pub/pdb/validation_reports/si/8sip | 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: Antibody | Mass: 23942.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24295.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-NOS / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 50 mM TRIS PH 8.3, 15% PEG 4000, 0.1 mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2023 |
Radiation | Monochromator: Kohzu HLD-15 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→57.04 Å / Num. obs: 30888 / % possible obs: 96.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.61 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1901 / Rpim(I) all: 0.06938 / Rrim(I) all: 0.2027 / Net I/σ(I): 6.33 |
Reflection shell | Resolution: 1.94→2.009 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.506 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 2931 / CC1/2: 0.586 / CC star: 0.86 / Rpim(I) all: 0.6427 / Rrim(I) all: 1.642 / % possible all: 91.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→57.04 Å / SU ML: 0.242 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.878 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→57.04 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: -12.0772151881 Å / Origin y: 23.4036181553 Å / Origin z: -3.77583644921 Å
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Refinement TLS group | Selection details: all |