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Yorodumi- PDB-1sqz: Design of specific inhibitors of Phopholipase A2: Crystal structu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sqz | ||||||
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Title | Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between Group II Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PHOSPHOLIPASE A2 / DEHYDRO-IARS / TOXIN / 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: 1.2 Å | ||||||
Authors | Singh, N. / Prem Kumar, R. / Somvanshi, R.K. / Bilgrami, S. / Ethayathulla, A.S. / Sharma, S. / Dey, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between GroupII Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution Authors: Singh, N. / Prem Kumar, R. / Somvanshi, R.K. / Bilgrami, S. / Ethayathulla, A.S. / Sharma, S. / Dey, 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 | 1sqz.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sqz.ent.gz | 31.6 KB | Display | PDB format |
PDBx/mmJSON format | 1sqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/1sqz ftp://data.pdbj.org/pub/pdb/validation_reports/sq/1sqz | HTTPS FTP |
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-Related structure data
Related structure data | 1fb2S 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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Details | The biological Unit is Monomer |
-Components
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Species: Daboia russellii / Strain: russellii / 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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.2M Ammonium sulphate,50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 203 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 29, 2003 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 40325 / Num. obs: 40325 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.082 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.2→1.24 Å / Mean I/σ(I) obs: 14 / Rsym value: 0.09 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FB2 Resolution: 1.2→17.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.853 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / 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: 14.267 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1531 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→17.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20 /
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