+Open data
-Basic information
Entry | Database: PDB / ID: 1irb | ||||||
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Title | CARBOXYLIC ESTER HYDROLASE | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / ENZYME / CARBOXYLIC ESTER HYDROLASE / LIPID DEGRADATION | ||||||
Function / homology | Function and homology information Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of fibroblast proliferation / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Sundaralingam, M. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Phospholipase A2 engineering. Deletion of the C-terminus segment changes substrate specificity and uncouples calcium and substrate binding at the zwitterionic interface. Authors: Huang, B. / Yu, B.Z. / Rogers, J. / Byeon, I.J. / Sekar, K. / Chen, X. / Sundaralingam, M. / Tsai, M.D. / Jain, M.K. #1: Journal: Biochemistry / Year: 1991 Title: Phospholipase A2 Engineering. X-Ray Structural and Functional Evidence for the Interaction of Lysine-56 with Substrates Authors: Noel, J.P. / Bingman, C.A. / Deng, T.L. / Dupureur, C.M. / Hamilton, K.J. / Jiang, R.T. / Kwak, J.G. / Sekharudu, C. / Sundaralingam, M. / Tsai, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1irb.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1irb.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 1irb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1irb_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
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Full document | 1irb_full_validation.pdf.gz | 416.3 KB | Display | |
Data in XML | 1irb_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1irb_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/1irb ftp://data.pdbj.org/pub/pdb/validation_reports/ir/1irb | HTTPS FTP |
-Related structure data
Related structure data | 2bppS 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: 13694.299 Da / Num. of mol.: 1 / Mutation: K120A, K121A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 / Gene: MATURE PLA2 / Organ: PANCREAS / Plasmid: PTO-A2MBL21 / Gene (production host): MATURE PLA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-[PLYSS] / References: UniProt: P00593, phospholipase A2 |
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#2: Chemical | ChemComp-CA / |
#3: 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: 2.38 Å3/Da / Density % sol: 48.22 % | ||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.2 Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS DESCRIBED FOR THE WILD TYPE ENZYME (NOEL ET AL., 1991), pH 7.2, vapor diffusion - hanging drop | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 26, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. obs: 10032 / % possible obs: 8 % / Redundancy: 2 % / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.3 / % possible all: 56 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 56 % |
-Processing
Software |
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Refinement | Starting model: WILD TYPE (PDB ENTRY 2BPP) Resolution: 1.9→8 Å / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.308 |