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Yorodumi- PDB-3g8f: Crystal structure of the complex formed between a group II phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g8f | |||||||||
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Title | Crystal structure of the complex formed between a group II phospholipase A2 and designed peptide inhibitor carbobenzoxy-dehydro-val-ala-arg-ser at 1.2 A resolution | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PHOSPHOLIPASE A2 / CRYSTAL STRUCTRE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Daboia russellii russellii (snake) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Singh, N. / Kaur, P. / Prem Kumar, R. / Somvanshi, R.K. / Perbandt, M. / Betzel, C. / Dey, S. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of the Complex Formed between a Group II Phospholipase A2 and Designed Peptide Inhibitor Carbobenzoxy-Dehydro-Val-Ala-Arg-Ser at 1.2 A Resolution Authors: Singh, N. / Kaur, P. / Prem Kumar, R. / Somvanshi, R.K. / Perband, M. / Betzel, C. / Dey, S. / Sharma, S. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g8f.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g8f.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 3g8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/3g8f ftp://data.pdbj.org/pub/pdb/validation_reports/g8/3g8f | HTTPS FTP |
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-Related structure data
Related structure data | 1skgS 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: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / References: UniProt: P59071, phospholipase A2 | ||
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#2: Protein/peptide | | ||
#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: 2.33 Å3/Da / Density % sol: 47.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M AMMONIUM SULPHATE, 30% PEG, CaCl2, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.806 / Wavelength: 0.803 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 5, 2003 / Details: MIRRORS | |||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.2→30 Å / Num. all: 35175 / Num. obs: 35175 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 20.5 | |||||||||
Reflection shell | Resolution: 1.2→1.27 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.487 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SKG Resolution: 1.25→29.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.917 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.049 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.28 Å / Total num. of bins used: 20 /
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