+Open data
-Basic information
Entry | Database: PDB / ID: 3w56 | ||||||
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Title | Structure of a C2 domain | ||||||
Components | C2 domain protein | ||||||
Keywords | LIPID BINDING PROTEIN / C2 domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Scophthalmus maximus (turbot) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Traore, D.A.K. / Whisstock, J.C. | ||||||
Citation | Journal: Biochem.J. / Year: 2013 Title: Defining the interaction of perforin with calcium and the phospholipid membrane. Authors: Traore, D.A. / Brennan, A.J. / Law, R.H. / Dogovski, C. / Perugini, M.A. / Lukoyanova, N. / Leung, E.W. / Norton, R.S. / Lopez, J.A. / Browne, K.A. / Yagita, H. / Lloyd, G.J. / Ciccone, A. / ...Authors: Traore, D.A. / Brennan, A.J. / Law, R.H. / Dogovski, C. / Perugini, M.A. / Lukoyanova, N. / Leung, E.W. / Norton, R.S. / Lopez, J.A. / Browne, K.A. / Yagita, H. / Lloyd, G.J. / Ciccone, A. / Verschoor, S. / Trapani, J.A. / Whisstock, J.C. / Voskoboinik, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w56.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w56.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 3w56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w56_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 3w56_full_validation.pdf.gz | 426.9 KB | Display | |
Data in XML | 3w56_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 3w56_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w56 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w56 | HTTPS FTP |
-Related structure data
Related structure data | 3w57C 3nsjS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15289.983 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scophthalmus maximus (turbot) / Gene: C2P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle / References: UniProt: E2FYL5 |
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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: 2.05 Å3/Da / Density % sol: 40.1 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 100mM Tris-HCl, 200mM MgCl2, 20% PEG 3350, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953697 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953697 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→47.027 Å / Num. all: 16003 / Num. obs: 16003 / % possible obs: 97.9 % / Redundancy: 4.6 % / Rsym value: 0.077 / Net I/σ(I): 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NSJ Resolution: 1.6→27.61 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.22 / σ(F): 0 / Phase error: 27.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.217 Å2 / ksol: 0.366 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.6 Å2 / Biso mean: 22.5196 Å2 / Biso min: 5.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→27.61 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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