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Yorodumi- PDB-1b4w: BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS-IMPLICATIONS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b4w | ||||||
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Title | BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS-IMPLICATIONS FOR ITS ASSOCIATION AND ANTICOAGULANT ACTIVITIES BY X-RAY CRYSTALLOGRAPHY | ||||||
Components | PROTEIN (PHOSPHOLIPASE A2) | ||||||
Keywords | HYDROLASE / BASIC PHOSPHOLIPASE A2 / AGKISTRODON HALYS PALLAS / DIMER / ANTICOAGULANT ACTIVITY | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Gloydius halys (Halys viper) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zhao, K.H. / Lin, Z.J. | ||||||
Citation | Journal: Toxicon / Year: 2000 Title: Structure of basic phospholipase A2 from Agkistrodon halys Pallas: implications for its association, hemolytic and anticoagulant activities. Authors: Zhao, K. / Zhou, Y. / Lin, Z. #1: Journal: SCI.CHINA, SER.C: LIFE SCI. / Year: 1999 Title: Refined Structure of Basic Phospholipase A2 from the Venom of Agkistrodon Halys Pallas in Orthorhombic Crystal Form I at 0.25Nm Resolution (in: C) Authors: Zhao, K.H. / Song, S.Y. / Lin, Z.J. / Zhou, Y.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b4w.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b4w.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b4w ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b4w | HTTPS FTP |
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-Related structure data
Related structure data | 1pp2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13923.168 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gloydius halys (Halys viper) / Cellular location: EXTRACELLULARGlossary of biology / Secretion: YES / References: UniProt: O42187, phospholipase A2 #2: Sugar | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 50 % Description: THE STRUCTURE OF BASIC PLA2 FROM AGKISTRODON HALYS PALLAS IN C2 CRYSTAL FORM WAS DETERMINED BY MOLECULAR REPLACEMENT METHOD, USING A CHAIN STRUCTURE OF THE SAME ENZYME IN P212121 CRYSTAL ...Description: THE STRUCTURE OF BASIC PLA2 FROM AGKISTRODON HALYS PALLAS IN C2 CRYSTAL FORM WAS DETERMINED BY MOLECULAR REPLACEMENT METHOD, USING A CHAIN STRUCTURE OF THE SAME ENZYME IN P212121 CRYSTAL FORM (PDB CODE 1JIA) AS SEARCH MODEL. | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: THE PROTEIN SOLUTIONS CONTAINED 0.1M LI2SO4, 9% PEG 4K AND 0.3% N-OCTYL BETA- D-GLUCOPYRANOSIDE IN 0.01M TRIS-HCL BUFFER(PH 8.5) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN ...Details: THE PROTEIN SOLUTIONS CONTAINED 0.1M LI2SO4, 9% PEG 4K AND 0.3% N-OCTYL BETA- D-GLUCOPYRANOSIDE IN 0.01M TRIS-HCL BUFFER(PH 8.5) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 18% PEG 4K IN SAME BUFFER, ROOM TEMPERATURE OF 17DEG.C. | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 15, 1997 |
Radiation | Monochromator: NICKEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 16462 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.087 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.368 / % possible all: 96.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 42427 |
Reflection shell | *PLUS % possible obs: 93.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PP2 Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.71 Å / Total num. of bins used: 1
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 9.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.387 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.314 |