+Open data
-Basic information
Entry | Database: PDB / ID: 8jh6 | ||||||||||||
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Title | Crystal structure of apixaban-bound racemic ABLE | ||||||||||||
Components |
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Keywords | DE NOVO PROTEIN / Small molecule-binding protein / Racemic protein | ||||||||||||
Function / homology | Chem-GG2 / polypeptide(D) / polypeptide(D) (> 10) / polypeptide(D) (> 100) Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Zhao, K. / Li, T. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Crystal structure of apixaban-bound racemic ABLE Authors: Zhao, K. / Li, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jh6.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jh6.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 8jh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jh6_validation.pdf.gz | 995.6 KB | Display | wwPDB validaton report |
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Full document | 8jh6_full_validation.pdf.gz | 998.7 KB | Display | |
Data in XML | 8jh6_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 8jh6_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/8jh6 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/8jh6 | 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: 13807.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: Protein | Mass: 13817.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||
#3: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium sulfate decahydrate, 20% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.42 Å / Num. obs: 20692 / % possible obs: 96.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1038 / Net I/σ(I): 16.65 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.517 / Num. unique obs: 2084 / CC1/2: 0.941 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.42 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→28.42 Å
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Refine LS restraints |
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LS refinement shell |
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