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Yorodumi- PDB-1zwp: The atomic resolution Crystal structure of the Phospholipase A2 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zwp | ||||||
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Title | The atomic resolution Crystal structure of the Phospholipase A2 (PLA2) complex with Nimesulide reveals its weaker binding to PLA2 | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE / Phospholipase A2 / Nimesulide / complex / 1.1A resolution | ||||||
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 pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: The atomic resolution Crystal structure of the Phospholipase A2 (PLA2) complex with Nimesulide reveals its weaker binding to PLA2 Authors: Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / 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 | 1zwp.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zwp.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/1zwp ftp://data.pdbj.org/pub/pdb/validation_reports/zw/1zwp | 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 pulchella (snake) / Species: Daboia russellii / Strain: Viper Russells / References: UniProt: P59071, phospholipase A2 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NIM / | #4: Chemical | ChemComp-MOH / | #5: 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: 49.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Mar 24, 2005 / 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: 1.1→52.2 Å / Num. all: 51783 / Num. obs: 51691 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.06 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.1→1.12 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 3426 / Rsym value: 0.372 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FB2 Resolution: 1.1→52.2 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.773 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.027 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.473 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→52.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.103→1.131 Å / Total num. of bins used: 20
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