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Yorodumi- PDB-5fx0: Fasciola hepatica calcium binding protein FhCaBP2: Structure of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fx0 | ||||||
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Title | Fasciola hepatica calcium binding protein FhCaBP2: Structure of the dynein light chain-like domain. P6422 native. | ||||||
Components | CALCIUM BINDING PROTEIN | ||||||
Keywords | CELL ADHESION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | FASCIOLA HEPATICA (liver fluke) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nguyen, T.H. / Thomas, C.M. / Timson, D.J. / van Raaij, M.J. | ||||||
Citation | Journal: Parasitol. Res. / Year: 2016 Title: Fasciola hepatica calcium-binding protein FhCaBP2: structure of the dynein light chain-like domain. Authors: Nguyen, T.H. / Thomas, C.M. / Timson, D.J. / van Raaij, M.J. #1: Journal: Parasitology / Year: 2015 Title: Fhcabp2: A Fasciola Hepatica Calcium-Binding Protein with EF-Hand and Dynein Light Chain Domains. Authors: Thomas, C.M. / Timson, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fx0.cif.gz | 33.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fx0.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fx0_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
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Full document | 5fx0_full_validation.pdf.gz | 418.1 KB | Display | |
Data in XML | 5fx0_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 5fx0_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fx0 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fx0 | HTTPS FTP |
-Related structure data
Related structure data | 5fwzSC 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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Unit cell |
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-Components
#1: Protein | Mass: 12522.271 Da / Num. of mol.: 1 / Fragment: DYNEIN LIGHT CHAIN-LIKE DOMAIN, RESIDUES 99-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) FASCIOLA HEPATICA (liver fluke) / Plasmid: PET46EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 / Variant (production host): DE3 / References: UniProt: A0A0B5GUS3 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUES AHHHHHHVDD |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.5 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 10 ML OF 10 MM TRIS-HCL PH 8.5, 50 MM SODIUM CHLORIDE, 20 % (W/V) PEG 3350, 0.2 M SODIUM TARTRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0047 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015 Details: SI(111) CHANNEL-CUT, CRYOCOOLEDELLIPTICALLY BENT VERTICAL AND HORIZONTAL FOCUSSING MIRRORS |
Radiation | Monochromator: SI(111) CHANNEL-CUT, CRYOCOOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0047 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 5253 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FWZ Resolution: 2.3→51.64 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.251 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.215 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→51.64 Å
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Refine LS restraints |
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