+Open data
-Basic information
Entry | Database: PDB / ID: 4qfv | ||||||
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Title | Crystal structure of a unique ankyrin | ||||||
Components | ANK-N5C-281 | ||||||
Keywords | DE NOVO PROTEIN / DESIGNED ANKYRIN REPEATS / DOMAIN SWAP | ||||||
Function / homology | Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / ACETATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å | ||||||
Authors | Ethayathulla, A.S. / Tikhonova, E.B. / Guan, L. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: A transcription blocker isolated from a designed repeat protein combinatorial library by in vivo functional screen. Authors: Tikhonova, E.B. / Ethayathulla, A.S. / Su, Y. / Hariharan, P. / Xie, S. / Guan, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qfv.cif.gz | 361.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qfv.ent.gz | 300.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/4qfv ftp://data.pdbj.org/pub/pdb/validation_reports/qf/4qfv | HTTPS FTP |
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-Related structure data
Related structure data | 4o60SC 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: 25111.428 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100 MM SODIUM ACETATE TRIHYDRATE (PH 4.5), 200 MM (NH4)2SO4, 16-18% PEG 3350, AND 10% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2014 / Details: Mirrors |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 56819 / Num. obs: 56375 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 22.5 Å2 / Rsym value: 0.07 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.63 / Num. unique all: 2735 / Rsym value: 0.5 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O60 Resolution: 1.999→48.735 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 27.07 / Stereochemistry target values: ML / Details: TLS refinement
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.999→48.735 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: 38.2352 Å / Origin y: 7.0529 Å / Origin z: 102.4424 Å
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Refinement TLS group | Selection details: all |