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Open data
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Basic information
Entry | Database: PDB / ID: 1mks | ||||||
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Title | CARBOXYLIC ESTER HYDROLASE, TRIGONAL FORM OF THE TRIPLE MUTANT | ||||||
![]() | PHOSPHOLIPASE A2 | ||||||
![]() | HYDROLASE / ENZYME / CARBOXYLIC ESTER HYDROLASE / TRIGONAL FORM | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Sundaralingam, M. | ||||||
![]() | ![]() Title: Phospholipase A2 engineering. Structural and functional roles of the highly conserved active site residue aspartate-99. Authors: Sekar, K. / Yu, B.Z. / Rogers, J. / Lutton, J. / Liu, X. / Chen, X. / Tsai, M.D. / Jain, M.K. / Sundaralingam, M. #1: ![]() 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. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.1 KB | Display | ![]() |
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PDB format | ![]() | 26.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.4 KB | Display | ![]() |
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Full document | ![]() | 415.8 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13777.520 Da / Num. of mol.: 1 / Mutation: Y52F, Y73F, D99N Source method: isolated from a genetically manipulated source Details: TRIGONAL FORM OF THE TRIPLE MUTANT / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||
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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 FROM DROPLETS CONTAINING 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML) 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 75% ...Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD FROM DROPLETS CONTAINING 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML) 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 75% MPD AND (50%) OF MPD IN THE RESERVOIR, 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: Dec 1, 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: 1.82→15 Å / Num. obs: 7346 / % possible obs: 8 % / Redundancy: 2 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.82→2 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 1.72 / % possible all: 29 |
Reflection | *PLUS % possible obs: 64 % / Num. measured all: 12043 |
Reflection shell | *PLUS % possible obs: 29 % |
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Processing
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Refinement | Method to determine structure: THE ATOMIC COORDINATES OF THE NEW HIGH RESOLUTION REFINEMENT OF THE TRIGONAL FORM OF THE NATIVE ENZYME WERE USED AS THE STARTING MODEL (PDB ENTRY 1MKT). Starting model: WILD TYPE 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 | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.312 |