+Open data
-Basic information
Entry | Database: PDB / ID: 5yv7 | ||||||
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Title | Racemic X-ray Structure of Calcicludine | ||||||
Components | Kunitz-type serine protease inhibitor homolog calcicludine | ||||||
Keywords | TOXIN / calcicludine / racemic crystal / L-type Ca2+ channels | ||||||
Function / homology | Function and homology information calcium channel regulator activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular space Similarity search - Function | ||||||
Biological species | Dendroaspis angusticeps (eastern green mamba) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.395 Å | ||||||
Authors | Shuai, G. / Qian, Q. / Lei, L. | ||||||
Citation | Journal: To Be Published Title: Racemic X-ray Structure of Calcicludine Authors: Shuai, G. / Qian, Q. / Lei, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yv7.cif.gz | 24.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yv7.ent.gz | 15.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/5yv7 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/5yv7 | HTTPS FTP |
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-Related structure data
Related structure data | 1bf0S S: Starting model for refinement |
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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: 6998.273 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Dendroaspis angusticeps (eastern green mamba) References: UniProt: P81658 |
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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: 3.25 Å3/Da / Density % sol: 62.15 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: sodium citrate tribasic dihydrate, 20% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.394→48 Å / Num. obs: 6918 / % possible obs: 99.3 % / Redundancy: 4.9 % / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.45→2.49 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BF0 Resolution: 2.395→47.995 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.395→47.995 Å
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Refine LS restraints |
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LS refinement shell |
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