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Yorodumi- PDB-1tdv: Non-specific binding to phospholipase A2:Crystal structure of the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tdv | ||||||
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Title | Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution | ||||||
Components |
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Keywords | HYDROLASE / NON-SPECIFIC / YWAAAA COMPLEX / PHOSPHOLIPASE A2 | ||||||
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 pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Singh, N. / Jabeen, T. / Ethayathulla, A.S. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Perbandt, M. / Betzel, C. / Singh, T.P. | ||||||
Citation | Journal: to be published Title: Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution Authors: Singh, N. / Jabeen, T. / Ethayathulla, A.S. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Perbandt, M. / 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 | 1tdv.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tdv.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 1tdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/1tdv ftp://data.pdbj.org/pub/pdb/validation_reports/td/1tdv | 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 pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2 | ||
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#2: Protein/peptide | Mass: 651.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ywaaaa peptide sequence was chemically synthesized | ||
#3: Chemical | ChemComp-SO4 / #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: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, 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 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 2004 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.806 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→51.99 Å / Num. all: 355374 / Num. obs: 14306 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 17.71 Å2 / Rsym value: 0.057 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 6.7 / Num. unique all: 721 / Rsym value: 0.342 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SKG Resolution: 1.7→51.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.739 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.105 / 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: 17.915 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→51.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å / Total num. of bins used: 20 /
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