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Yorodumi- PDB-1mkv: CARBOXYLIC ESTER HYDROLASE COMPLEX (PLA2 + TRANSITION STATE ANALO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mkv | ||||||
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Title | CARBOXYLIC ESTER HYDROLASE COMPLEX (PLA2 + TRANSITION STATE ANALOG COMPLEX) | ||||||
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 / phospholipase A2 ...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 / phospholipase A2 / bile acid binding / calcium-dependent phospholipase A2 activity / 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 WILD TYPE / Resolution: 1.89 Å | ||||||
Authors | Sundaralingam, M. | ||||||
Citation | 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. #1: Journal: To be Published Title: 1.72 Angstrom Resolution Refinement of the Trigonal Form of Bovine Pancreatic Phospholipase A2 Authors: Sekar, K. / Sekharudu, C. / Tsai, M.-D. / Sundaralingam, M. #2: 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. #3: 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. #4: 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. #5: 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 | 1mkv.cif.gz | 41.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mkv.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1mkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mkv_validation.pdf.gz | 683.1 KB | Display | wwPDB validaton report |
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Full document | 1mkv_full_validation.pdf.gz | 686.1 KB | Display | |
Data in XML | 1mkv_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1mkv_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mkv ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mkv | 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: 13810.504 Da / Num. of mol.: 1 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: Chemical | ChemComp-GEL / |
#4: 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: 2.33 Å3/Da / Density % sol: 47.27 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (20MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS ...Details: CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (20MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.5 (MICRO)L OF 75% MPD AND 2.0 (MICRO)L OF (2MM) IN THE DROPLET. THE RESERVOIR CONTAINED (50%) OF MPD., pH 7.5, 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 | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Date: Nov 8, 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: 1.89→15 Å / Num. obs: 8758 / % possible obs: 8 % / Redundancy: 5 % / Rsym value: 0.071 |
Reflection shell | Resolution: 1.89→2.01 Å / Rsym value: 0.434 |
Reflection | *PLUS % possible obs: 72 % / Num. measured all: 44425 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: THE HIGH RESOLUTION ATOMIC COORDINATES OF THE WILD TYPE Starting model: WILD TYPE Resolution: 1.89→8 Å / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.97 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 Num. reflection obs: 7726 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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