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Yorodumi- PDB-1ceh: STRUCTURE AND FUNCTION OF THE CATALYTIC SITE MUTANT ASP99ASN OF P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ceh | ||||||
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Title | STRUCTURE AND FUNCTION OF THE CATALYTIC SITE MUTANT ASP99ASN OF PHOSPHOLIPASE A2: ABSENCE OF CONSERVED STRUCTURAL WATER | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE (CARBOXYLIC ESTER) | ||||||
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 / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 | Kumar, A. / Sekharudu, C. / Ramakrishnan, B. / Dupureur, C.M. / Zhu, H. / Tsai, M.-D. / Sundaralingam, M. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: Structure and function of the catalytic site mutant Asp 99 Asn of phospholipase A2: absence of the conserved structural water. Authors: Kumar, A. / Sekharudu, C. / Ramakrishnan, B. / Dupureur, C.M. / Zhu, H. / Tsai, M.D. / Sundaralingam, M. #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. / 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 | 1ceh.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ceh.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ceh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ceh_validation.pdf.gz | 414.7 KB | Display | wwPDB validaton report |
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Full document | 1ceh_full_validation.pdf.gz | 417.8 KB | Display | |
Data in XML | 1ceh_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1ceh_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/1ceh ftp://data.pdbj.org/pub/pdb/validation_reports/ce/1ceh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13809.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.77 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.6 / Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 10307 / % possible obs: 98.7 % |
Reflection | *PLUS Highest resolution: 1.9 Å / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Resolution: 1.9→6.5 Å / σ(F): 3
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Displacement parameters | Biso mean: 27.6 Å2 | ||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6.5 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.185 / Rfactor Rwork: 0.185 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |