+Open data
-Basic information
Entry | Database: PDB / ID: 6lfp | |||||||||
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Title | Cry3Aa protein for enzyme entrapment | |||||||||
Components | Cry3Aa protein | |||||||||
Keywords | TOXIN / Pesticidal / Crystal forming / Nanoporous / Protein entrapment | |||||||||
Function / homology | Function and homology information symbiont-mediated cytolysis of host cell / sporulation resulting in formation of a cellular spore / : / toxin activity / signaling receptor binding / membrane Similarity search - Function | |||||||||
Biological species | Bacillus thuringiensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å | |||||||||
Authors | Heater, B.S. / Chan, M.K. | |||||||||
Funding support | Hong Kong, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: In Vivo Enzyme Entrapment in a Protein Crystal. Authors: Heater, B.S. / Yang, Z. / Lee, M.M. / Chan, M.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lfp.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lfp.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/6lfp ftp://data.pdbj.org/pub/pdb/validation_reports/lf/6lfp | HTTPS FTP |
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-Related structure data
Related structure data | 1dlcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 73177.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry3Aa, EEL55_22485 / Plasmid: pHT315 / Production host: Bacillus thuringiensis (bacteria) / Strain (production host): israelensi / References: UniProt: Q9S6N9, UniProt: P0A381*PLUS |
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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: 2.71 Å3/Da / Density % sol: 59.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1M NaOAc pH 4.8, 2.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 10, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.31→87.46 Å / Num. obs: 12048 / % possible obs: 98.9 % / Redundancy: 3.9 % / CC1/2: 0.979 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.08 / Rrim(I) all: 0.163 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DLC Resolution: 3.31→38.34 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.176 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.3 Å2 / Biso mean: 33.788 Å2 / Biso min: 13.96 Å2
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Refinement step | Cycle: final / Resolution: 3.31→38.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.311→3.397 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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