+Open data
-Basic information
Entry | Database: PDB / ID: 2wg8 | ||||||
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Title | Structure of Oryza Sativa (Rice) PLA2, orthorhombic crystal form | ||||||
Components | (PUTATIVE PHOSPHOLIPASE A2) x 2 | ||||||
Keywords | HYDROLASE / SECRETORY PLA2 | ||||||
Function / homology | Function and homology information phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / lipid binding / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ORYZA SATIVA (Asian cultivated rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Guy, J.E. / Stahl, U. / Lindqvist, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structure of a Class Xib Phospholipase A2 (Pla2): Rice (Oryza Sativa) Isoform-2 Pla2 and an Octanoate Complex. Authors: Guy, J.E. / Stahl, U. / Lindqvist, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wg8.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wg8.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 2wg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wg8_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 2wg8_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 2wg8_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2wg8_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wg8 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wg8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS
NCS ensembles :
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-Components
#1: Protein | Mass: 13937.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: Q9XG81, phospholipase A2 | ||||||||
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#2: Protein | Mass: 13923.841 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: Q9XG81, phospholipase A2 #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | ACCESSION NUMBER PROVIDED BY AUTHOR IS NCBI REFERENCE NP_001049620.1. THE DEPOSITED SEQUENCE ...ACCESSION NUMBER PROVIDED BY AUTHOR IS NCBI REFERENCE NP_001049620.1. THE DEPOSITED SEQUENCE INCLUDES THE SIGNAL SEQUENCE, OUR CONSTRUCT DOES NOT. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: VAPOUR DIFFUSION, 20 DEGREES. WELL CONTAINED 0.75ML OF SOLN A (16-18% PEG3350, 0.1M BISTRISPROPANE PH 6.5, 0.2M POTASSIUM THIOCYANATE) AND 0.25ML OF SOLN B (0.1M SODIUM ACETATE PH 4.6, 2M SODIUM CHLORIDE) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 15584 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.4 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: P62 CRYSTAL FORM Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 11.555 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.243 / 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: 26.486 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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