[English] 日本語
Yorodumi- PDB-1kvw: CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT H48Q OF BOVINE PANCREAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kvw | ||||||
---|---|---|---|---|---|---|---|
Title | CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT H48Q OF BOVINE PANCREATIC PLA2 ENZYME | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / ENZYME / CARBOXYLIC ESTER HYDROLASE | ||||||
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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process ...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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / 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 / 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 / THE COORDINATES OF THE WILD TYPE (PDB ENTRY 1MKT) WERE USED AS THE STARTING MODEL FOR REFINEMENT. / Resolution: 1.95 Å | ||||||
Authors | Sundaralingam, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2. Authors: Sekar, K. / Biswas, R. / Li, Y. / Tsai, M. / Sundaralingam, M. #1: Journal: To be Published Title: The High Resolution Refinement of the Orthorhombic Bovine Pancreatic Phospholipase A2 Authors: Sekar, K. / Sundaralingam, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structure of the Complex of Bovine Pancreatic Phospholipase A2 with a Transition-State Analogue Authors: Sekar, K. / Kumar, A. / Liu, X. / Tsai, M.D. / Gelb, M.H. / Sundaralingam, M. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: 1.72 A Resolution Refinement of the Trigonal Form of Bovine Pancreatic Phospholipase A2 Authors: Sekar, K. / Sekharudu, C. / Tsai, M. / Sundaralingam, M. #4: Journal: Biochemistry / Year: 1997 Title: Crystal Structure of the Complex of Bovine Pancreatic Phospholipase A2 with the Inhibitor 1-Hexadecyl-3-(Trifluoroethyl)-Sn-Glycero-2-Phosphomethanol Authors: Sekar, K. / Eswaramoorthy, S. / Jain, M.K. / Sundaralingam, M. #5: Journal: Biochemistry / Year: 1997 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. #6: 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. #7: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kvw.cif.gz | 36 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kvw.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvw ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvw | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kvxC 1kvyC 1mktS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13800.485 Da / Num. of mol.: 1 / Mutation: H48Q 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 |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion / pH: 7.2 Details: CRYSTALS WERE GROWN BY THE VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 40% ...Details: CRYSTALS WERE GROWN BY THE VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 40% MPD AND (60%) OF MPD IN THE RESERVOIR, vapor diffusion | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 291 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 15, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→10 Å / Num. obs: 7424 / % possible obs: 73 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.082 |
Reflection shell | Resolution: 1.95→2.04 Å / Rmerge(I) obs: 0.218 / % possible all: 50 |
Reflection | *PLUS Num. measured all: 21567 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: THE COORDINATES OF THE WILD TYPE (PDB ENTRY 1MKT) WERE USED AS THE STARTING MODEL FOR REFINEMENT. Starting model: RECOMBINANT PLA2 (1MKT) Resolution: 1.95→10 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.04 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|