+Open data
-Basic information
Entry | Database: PDB / ID: 6w70 | ||||||
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Title | Crystal Structure of apixaban-bound ABLE | ||||||
Components | De novo designed ABLE | ||||||
Keywords | DE NOVO PROTEIN / 4-helix bundle / de novo / ligand-binding | ||||||
Function / homology | ACETATE ION / Chem-GG2 Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.296 Å | ||||||
Authors | Polizzi, N.F. | ||||||
Funding support | 1items
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Citation | Journal: Science / Year: 2020 Title: A defined structural unit enables de novo design of small-molecule-binding proteins. Authors: Polizzi, N.F. / DeGrado, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w70.cif.gz | 156.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w70.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 6w70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w70_validation.pdf.gz | 947.2 KB | Display | wwPDB validaton report |
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Full document | 6w70_full_validation.pdf.gz | 951.3 KB | Display | |
Data in XML | 6w70_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 6w70_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w70 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w70 | HTTPS FTP |
-Related 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: 13817.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.06 Å3/Da / Density % sol: 40.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.6 M AmSO4, 0.1 M Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.292→41.259 Å / Num. all: 54993 / Num. obs: 54993 / % possible obs: 97.5 % / Redundancy: 10.7 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.124 / Rsym value: 0.111 / Net I/av σ(I): 3.3 / Net I/σ(I): 27.9 / Num. measured all: 587522 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Designed model Resolution: 1.296→41.259 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.33 / 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: 121.41 Å2 / Biso mean: 20.1028 Å2 / Biso min: 8.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.296→41.259 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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