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Yorodumi- PDB-1oxl: INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oxl | ||||||
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Title | INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE / phospholipase A2 / indole derivative / inhibition | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Daboia russellii russellii (snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chandra, V. / Balasubramanya, R. / Kaur, P. / Singh, T.P. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2005 Title: Crystal structure of the complex of the secretory phospholipase A2 from Daboia russelli pulchella with an endogenic indole derivative, 2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl-acetic ...Title: Crystal structure of the complex of the secretory phospholipase A2 from Daboia russelli pulchella with an endogenic indole derivative, 2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl-acetic acid at 1.8 A resolution. Authors: Balasubramanya, R. / Chandra, V. / Kaur, P. / Singh, T.P. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Regulation of catalytic function by molecular association: Crystal structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 resolution Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C.H. / Singh, T.P. #2: Journal: J.Mol.Biol. / Year: 2000 Title: Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from daboia russelli pulchella at 2.4 resolution Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / 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 | 1oxl.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oxl.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/1oxl ftp://data.pdbj.org/pub/pdb/validation_reports/ox/1oxl | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Secretion: venom / Species: Daboia russellii / Strain: russellii / References: UniProt: P59071, phospholipase A2 #2: Chemical | ChemComp-IDA / ( | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2 Ammonium sulphate buffer with 20mm sodium cacodylate, 50mm calcium chloride, 3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.91 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 2001 / Details: Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 21615 / Num. obs: 21615 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 23.59 Å2 / Rsym value: 0.031 / Net I/σ(I): 39.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.083 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FB2 Resolution: 1.8→19.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.697 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.139 / 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: 24.094 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
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