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Yorodumi- PDB-1jq9: Crystal structure of a complex formed between phospholipase A2 fr... -
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-Basic information
Entry | Database: PDB / ID: 1jq9 | ||||||
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Title | Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / phospholipase A2 / Daboia russelli pulchella / neurotoxic / designed peptide / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonate 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 pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Betzel, C. / Singh, T.P. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2002 Title: Crystal Structure of a Complex Formed between a Snake Venom Phospholipase A2 and a Potent Peptide Inhibitor Phe-Leu-Ser-Tyr-Lys at 1.8 A Resolution Authors: Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Perbandt, M. / Srinivasan, A. / Betzel, C. / Singh, T.P. #1: 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. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C. / Singh, T.P. #3: Journal: J.MOL.BIOL. / Year: 2002 Title: First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between ...Title: First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution Authors: Chandra, V. / Jasti, J. / Kaur, P. / Betzel, C. / Srinivasan, A. / Singh, T.P. #4: Journal: Biochemistry / Year: 2002 Title: Structural basis of phospholipase A2 inhibition for the synthesis of prostaglandins by the plant alkaloid aristolochic acid from a 1.7 A crystal structure Authors: Chandra, V. / Jasti, J. / Kaur, P. / Srinivasan, A. / Betzel, C. / Singh, T.P. #5: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS) Authors: Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Srinivasan, A. / Betzel, C. / 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 | 1jq9.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jq9.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1jq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jq9_validation.pdf.gz | 394.5 KB | Display | wwPDB validaton report |
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Full document | 1jq9_full_validation.pdf.gz | 401 KB | Display | |
Data in XML | 1jq9_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1jq9_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jq9 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jq9 | HTTPS FTP |
-Related structure data
Related structure data | 1fe7 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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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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Details | The two protein chains (A and B) represent the two molecules in the asymmetric unit, with the A molecule containing peptide inhibitor |
-Components
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2 #2: Protein/peptide | | Mass: 657.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE SEQUENCE WAS CHEMICALLY SYNTHESIZED. #3: Chemical | ChemComp-ACY / #4: 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: 2.53 Å3/Da / Density % sol: 51.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 239988 / Num. obs: 239988 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.04 / Net I/σ(I): 9.44 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 4.7 / Mean I/σ(I) obs: 9.9 / Num. unique all: 1581 / Rsym value: 0.09 / % possible all: 98 |
Reflection | *PLUS Num. obs: 22959 / Num. measured all: 239988 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 98 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FE7 1fe7 Resolution: 1.8→11.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2042260.78 / Data cutoff high rms absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0477 Å2 / ksol: 0.332842 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→11.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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