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Yorodumi- PDB-7jtn: Human Complement Factor B Inhibited by a Slow Off-Rate Modified A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jtn | |||||||||
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Title | Human Complement Factor B Inhibited by a Slow Off-Rate Modified Aptamer of 29 Bases | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/DNA / Complement / Protease / Convertase / Inhibitor / Aptamer / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex | |||||||||
Function / homology | Function and homology information alternative-complement-pathway C3/C5 convertase / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity ...alternative-complement-pathway C3/C5 convertase / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | |||||||||
Authors | Xu, X. / Geisbrecht, B.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Immunol. / Year: 2021 Title: Inhibition of the Complement Alternative Pathway by Chemically Modified DNA Aptamers That Bind with Picomolar Affinity to Factor B. Authors: Xu, X. / Zhang, C. / Denton, D.T. / O'Connell, D. / Drolet, D.W. / Geisbrecht, B.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jtn.cif.gz | 327.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jtn.ent.gz | 263.2 KB | Display | PDB format |
PDBx/mmJSON format | 7jtn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jtn_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 7jtn_full_validation.pdf.gz | 563.5 KB | Display | |
Data in XML | 7jtn_validation.xml.gz | 62.2 KB | Display | |
Data in CIF | 7jtn_validation.cif.gz | 80.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/7jtn ftp://data.pdbj.org/pub/pdb/validation_reports/jt/7jtn | HTTPS FTP |
-Related structure data
Related structure data | 7jtqC 2ok5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 85641.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase #2: DNA chain | Mass: 10761.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SL1103 / Source: (synth.) synthetic construct (others) 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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M bis-tris, 0.2 M ammonium acetate, 25% peg-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97243 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→50 Å / Num. obs: 36509 / % possible obs: 99.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.101 / Rrim(I) all: 0.248 / Χ2: 0.923 / Net I/σ(I): 4.7 / Num. measured all: 209444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OK5 Resolution: 3.1→42.9 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.59 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.84 Å2 / Biso mean: 60.891 Å2 / Biso min: 16.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→42.9 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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