+Open data
-Basic information
Entry | Database: PDB / ID: 1faz | ||||||
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Title | THE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2 | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / phospholipase A2 / prokaryote / Streptomyces violaceoruber | ||||||
Function / homology | Function and homology information phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces violaceoruber (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | ||||||
Authors | Matoba, Y. / katsube, Y. / Sugiyama, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The crystal structure of prokaryotic phospholipase A2. Authors: Matoba, Y. / Katsube, Y. / Sugiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1faz.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1faz.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1faz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1faz_validation.pdf.gz | 358.9 KB | Display | wwPDB validaton report |
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Full document | 1faz_full_validation.pdf.gz | 360.3 KB | Display | |
Data in XML | 1faz_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 1faz_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/1faz ftp://data.pdbj.org/pub/pdb/validation_reports/fa/1faz | HTTPS FTP |
-Related 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: 13570.782 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces violaceoruber (bacteria) / Description: SECRETED / Plasmid: PIJ680 / Production host: Streptomyces lividans (bacteria) References: UniProt: Q9Z4W2, UniProt: Q6UV28*PLUS, phospholipase A2 |
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#2: 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: 1.85 Å3/Da / Density % sol: 33.36 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, lithium sulfate, sodium cacodylate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 297 K / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. all: 16049 / Num. obs: 15558 / % possible obs: 77.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.41 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.276 / Num. unique all: 1174 / % possible all: 61.1 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 22015 / Rmerge(I) obs: 0.0741 |
-Processing
Software |
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Refinement | Resolution: 1.4→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 13.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 9.8 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.244 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.239 |