+Open data
-Basic information
Entry | Database: PDB / ID: 6i8x | |||||||||
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Title | As-p18, an extracellular fatty acid binding protein | |||||||||
Components | Fatty acid-binding protein homolog | |||||||||
Keywords | LIPID BINDING PROTEIN / Extracellular / nematodes / fatty acid binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Ascaris suum (pig roundworm) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Gabrielsen, M. / Riboldi-Tunnicliffe, A. / Ibanez-Shimabukuro, M. / Smith, B.O. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Biosci.Rep. / Year: 2019 Title: As-p18, an extracellular fatty acid binding protein of nematodes, exhibits unusual structural features. Authors: Ibanez-Shimabukuro, M. / Rey-Burusco, M.F. / Gabrielsen, M. / Franchini, G.R. / Riboldi-Tunnicliffe, A. / Roe, A.J. / Griffiths, K. / Cooper, A. / Corsico, B. / Kennedy, M.W. / Smith, B.O. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2012 Title: Useable diffraction data from a multiple microdomain-containing crystal of Ascaris suum As-p18 fatty-acid-binding protein using a microfocus beamline. Authors: Gabrielsen, M. / Riboldi-Tunnicliffe, A. / Ibanez-Shimabukuro, M. / Griffiths, K. / Roe, A.J. / Cooper, A. / Smith, B.O. / Corsico, B. / Kennedy, M.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i8x.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i8x.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 6i8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i8x_validation.pdf.gz | 953.4 KB | Display | wwPDB validaton report |
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Full document | 6i8x_full_validation.pdf.gz | 957 KB | Display | |
Data in XML | 6i8x_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6i8x_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/6i8x ftp://data.pdbj.org/pub/pdb/validation_reports/i8/6i8x | HTTPS FTP |
-Related structure data
Related structure data | 6i9fC 1g74S 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: 17637.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ascaris suum (pig roundworm) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P55776 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 3.97 Å3/Da / Density % sol: 69.03 % / Description: Square cuboid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 40% ethylene glycol, 0.1 M acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20.06 Å / Num. obs: 23648 / % possible obs: 93.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.52 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.104 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Rpim(I) all: 0.435 / Rrim(I) all: 0.679 / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G74 Resolution: 2.3→14.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.171
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Displacement parameters | Biso mean: 47.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→14.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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