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Yorodumi- PDB-5fwz: Fasciola hepatica calcium binding protein FhCaBP2: Structure of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fwz | ||||||
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Title | Fasciola hepatica calcium binding protein FhCaBP2: Structure of the dynein light chain-like domain. P41212 mercury derivative. | ||||||
Components | CALCIUM BINDING PROTEIN | ||||||
Keywords | CALCIUM-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | FASCIOLA HEPATICA (liver fluke) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 | 5fwz.cif.gz | 34.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fwz.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fwz_validation.pdf.gz | 417.5 KB | Display | wwPDB validaton report |
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Full document | 5fwz_full_validation.pdf.gz | 418.1 KB | Display | |
Data in XML | 5fwz_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 5fwz_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/5fwz ftp://data.pdbj.org/pub/pdb/validation_reports/fw/5fwz | HTTPS FTP |
-Related 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: 11488.179 Da / Num. of mol.: 1 / Fragment: DYNEIN LIGHT CHAIN-LIKE DOMAIN, RESIDUES 92-189 Source method: isolated from a genetically manipulated source Details: THE PURIFIED PROTEIN CONTAIN ALSO THE N- TERMINAL HIS-TAG AND EF-HAND DOMAIN, HOWEVER WE BELIEVE THIS WAS PROTEOLYSED IN SITU IN THE CRYSTALLIZATION DROP. THEREFORE ONLY OBSERVED RESIDUES ...Details: THE PURIFIED PROTEIN CONTAIN ALSO THE N- TERMINAL HIS-TAG AND EF-HAND DOMAIN, HOWEVER WE BELIEVE THIS WAS PROTEOLYSED IN SITU IN THE CRYSTALLIZATION DROP. THEREFORE ONLY OBSERVED RESIDUES ARE GIVEN. FOR MORE DETAILS SEE THE PRIMARY REFERENCE. 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: Chemical | ChemComp-HG / | ||
#3: Chemical | #4: 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: 3.2 Å3/Da / Density % sol: 61.3 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 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: 1.0056 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015 Details: ELLIPTICALLY 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: 1.0056 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→23 Å / Num. obs: 7026 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.3→22.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.264 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.212 / 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: 36.662 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→22.83 Å
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Refine LS restraints |
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