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Yorodumi- PDB-1kvx: CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT D99A OF BOVINE PANCREAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kvx | ||||||
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Title | CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT D99A OF BOVINE PANCREATIC PLA2, 1.9 A ORTHORHOMBIC FORM | ||||||
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 / 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 / THE HIGH RESOLUTION ATOMIC COORDINATES OF THE ORTHORHOMBIC FORM OF THE RECOMBINANT ENZYME (PDB ENTRY 1UNE) WERE USED AS THE STARTING MODEL FOR THE REFINEMENT. / Resolution: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kvx.cif.gz | 36.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kvx.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kvx_validation.pdf.gz | 359.8 KB | Display | wwPDB validaton report |
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Full document | 1kvx_full_validation.pdf.gz | 362 KB | Display | |
Data in XML | 1kvx_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1kvx_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvx ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvx | HTTPS FTP |
-Related structure data
Related structure data | 1kvwC 1kvyC 1uneS S: Starting model for refinement C: citing same article (ref.) |
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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: 13766.494 Da / Num. of mol.: 1 / Mutation: D99A 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: 2.07 Å3/Da / Density % sol: 40.68 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.2 Details: CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE PROTEIN (15 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH ...Details: CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE PROTEIN (15 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.0 (MICRO)L OF 50% MPD IN THE DROPLET. THE RESERVOIR CONTAINED (75%) OF MPD., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / 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 | Source: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 28, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→10 Å / Num. obs: 8110 / % possible obs: 86 % / Redundancy: 2 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 1.9→1.99 Å / Rmerge(I) obs: 0.192 / % possible all: 83 |
Reflection | *PLUS Num. measured all: 20534 |
-Processing
Software |
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Refinement | Method to determine structure: THE HIGH RESOLUTION ATOMIC COORDINATES OF THE ORTHORHOMBIC FORM OF THE RECOMBINANT ENZYME (PDB ENTRY 1UNE) WERE USED AS THE STARTING MODEL FOR THE REFINEMENT. Starting model: WILD TYPE, PDB ENTRY 1UNE Resolution: 1.9→10 Å / Rfactor Rfree error: 0.24 / Data cutoff high absF: 0.1 / Data cutoff low absF: 1000000 / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 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: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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