+Open data
-Basic information
Entry | Database: PDB / ID: 5bvl | ||||||
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Title | Crystal structure of a de novo designed TIM-barrel | ||||||
Components | designed TIM barrel sTIM11 | ||||||
Keywords | DE NOVO PROTEIN / TIM-barrel / computational design / idealized scaffold | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.992 Å | ||||||
Authors | Feldmeier, K. / Hocker, B. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Authors: Huang, P.S. / Feldmeier, K. / Parmeggiani, F. / Fernandez Velasco, D.A. / Hocker, B. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bvl.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bvl.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 5bvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bvl_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 5bvl_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 5bvl_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 5bvl_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/5bvl ftp://data.pdbj.org/pub/pdb/validation_reports/bv/5bvl | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 22896.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.7 % / Description: Needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 25% PEG 3350, 0.2M magnesium chloride hexahydrate, 0.1M bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2014 |
Radiation | Monochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.992→46.79 Å / Num. obs: 11894 / % possible obs: 98.26 % / Redundancy: 5.86 % / Biso Wilson estimate: 41.84 Å2 / Rmerge(I) obs: 0.05804 / Net I/σ(I): 15.24 |
Reflection shell | Resolution: 1.992→2.064 Å / Rmerge(I) obs: 0.6607 / Mean I/σ(I) obs: 1.79 / % possible all: 93.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Rosetta backbone model Resolution: 1.992→46.79 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.25 / 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 mean: 61.9 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.992→46.79 Å
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Refine LS restraints |
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LS refinement shell |
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