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Yorodumi- PDB-4qmc: Crystal structure of complex formed between phospholipase A2 and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qmc | ||||||
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Title | Crystal structure of complex formed between phospholipase A2 and Biotin-sulfoxide at 1.09 A Resolution | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE | ||||||
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: 1.09 Å | ||||||
Authors | Shukla, P.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be published Title: Crystal structure of complex formed between phospholipase A2 and Biotin-sulfoxide at 1.09 A Resolution Authors: Shukla, P.K. / Sinha, M. / Kaur, P. / Sharma, 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 | 4qmc.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qmc.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/4qmc ftp://data.pdbj.org/pub/pdb/validation_reports/qm/4qmc | 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) References: UniProt: D0VX11, UniProt: P59071*PLUS, phospholipase A2 |
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-Non-polymers , 5 types, 278 molecules
#2: Chemical | ChemComp-GOL / |
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#3: Chemical | ChemComp-BSO / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-ACT / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | THIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE ...THIS COORDINATE |
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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: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulphate, PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 9, 2014 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→51.81 Å / Num. obs: 52702 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.058 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.09→1.118 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FB2 Resolution: 1.09→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.575 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.035 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 23.291 Å2
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Refinement step | Cycle: LAST / Resolution: 1.09→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.09→1.118 Å / Total num. of bins used: 20
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