+Open data
-Basic information
Entry | Database: PDB / ID: 3qrx | ||||||
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Title | Chlamydomonas reinhardtii centrin bound to melittin | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/TOXIN / calcium-binding / EF-hand / cell division / calcium binding / METAL BINDING PROTEIN-TOXIN complex | ||||||
Function / homology | Function and homology information inner dynein arm / dynein heavy chain binding / other organism cell membrane / porin activity / molecular function inhibitor activity / protein kinase inhibitor activity / pore complex / localization / monoatomic ion transport / centriole ...inner dynein arm / dynein heavy chain binding / other organism cell membrane / porin activity / molecular function inhibitor activity / protein kinase inhibitor activity / pore complex / localization / monoatomic ion transport / centriole / mitotic cell cycle / toxin activity / killing of cells of another organism / cell division / lipid binding / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Schreiter, E.R. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: The structure, molecular dynamics, and energetics of centrin-melittin complex. Authors: Sosa Ldel, V. / Alfaro, E. / Santiago, J. / Narvaez, D. / Rosado, M.C. / Rodriguez, A. / Gomez, A.M. / Schreiter, E.R. / Pastrana-Rios, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qrx.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qrx.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/3qrx ftp://data.pdbj.org/pub/pdb/validation_reports/qr/3qrx | HTTPS FTP |
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-Related structure data
Related structure data | 1cdmS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19488.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: VFL2, CHLREDRAFT_159554 / Plasmid: pT7-5 / Production host: Escherichia coli (E. coli) / References: UniProt: A8JC40, UniProt: P05434*PLUS | ||
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#2: Protein/peptide | Mass: 2852.487 Da / Num. of mol.: 1 / Fragment: residues 44-69 / Source method: obtained synthetically Details: Synthesized peptide corresponding to amino acids 44-69 of honey bee melittin References: UniProt: P01501 | ||
#3: Chemical | ChemComp-CA / #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: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 L of the Crcen-MLT (1:1.5 molar ratio, 10mg/mL total) solution with 2 L of a precipitant solution containing 50 mM HEPES, pH 7.5, 0.2 M KCl, and 40% v/v pentaerythritol propoxylate (5/4 ...Details: 2 L of the Crcen-MLT (1:1.5 molar ratio, 10mg/mL total) solution with 2 L of a precipitant solution containing 50 mM HEPES, pH 7.5, 0.2 M KCl, and 40% v/v pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 4, 2005 / Details: mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 10620 / Num. obs: 10334 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.2→2.26 Å / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CDM Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.885 / SU B: 8.828 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.754 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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