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Yorodumi- PDB-2dpq: The crystal structures of the calcium-bound con-G and con-T(K7gam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dpq | ||||||
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Title | The crystal structures of the calcium-bound con-G and con-T(K7gamma) dimeric peptides demonstrate a novel metal-dependent helix-forming motif | ||||||
Components | Conantokin-G | ||||||
Keywords | METAL BINDING PROTEIN / conantoxin / con-G / NMDAR antagonist / Gla-containing | ||||||
Function / homology | Conantokin, conserved site / Conantokin family signature. / host cell postsynaptic membrane / ion channel regulator activity / toxin activity / extracellular region / metal ion binding / Conantokin-G Function and homology information | ||||||
Biological species | Conus geographus (geography cone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Cnudde, S.E. / Prorok, M. / Dai, Q. / Castellino, F.J. / Geiger, J.H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: The crystal structures of the calcium-bound con-G and con-T[K7gamma] dimeric peptides demonstrate a metal-dependent helix-forming motif Authors: Cnudde, S.E. / Prorok, M. / Dai, Q. / Castellino, F.J. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dpq.cif.gz | 23.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dpq.ent.gz | 15.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dpq ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dpq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | In the presence of calcium, con-G forms an antiparallel dimeric structure. |
-Components
#1: Protein/peptide | Mass: 2265.196 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The con-G peptide was synthesized. The sequence of the peptide is naturally found in Conus geographus (geography cone) Source: (synth.) Conus geographus (geography cone) / References: UniProt: P07231 | ||
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#2: Chemical | ChemComp-CL / | ||
#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: 2.23 Å3/Da / Density % sol: 44.76 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 / Details: 35% dioxane, pH 8, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 12, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 12427 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.081 / Χ2: 1.036 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.923 / Num. unique all: 611 / Χ2: 0.353 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 14-mer polyalanine helix Resolution: 1.25→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.161 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→8 Å
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Refine LS restraints |
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