+Open data
-Basic information
Entry | Database: PDB / ID: 1mc2 | ||||||
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Title | monomeric LYS-49 phospholipase A2 homologue purified from AG | ||||||
Components | Acutohaemonlysin | ||||||
Keywords | TOXIN / YS49-PHOSPHOLIPASE A2 / SNAKE VENOM / AGKISTRODON ACUTUS | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Deinagkistrodon acutus (Chinese moccasin) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.85 Å | ||||||
Authors | Liu, Q. / Huang, Q.Q. / Zhang, R.G. / Weeks, C.M. / Jelsch, C. / Teng, M.K. / Niu, L.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The crystal structure of a novel, inactive, lysine 49 PLA2 from Agkistrodon acutus venom: an ultrahigh resolution, AB initio structure determination Authors: Liu, Q. / Huang, Q.Q. / Teng, M.K. / Weeks, C.M. / Jelsch, C. / Zhang, R.G. / Niu, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mc2.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mc2.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mc2_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
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Full document | 1mc2_full_validation.pdf.gz | 423.8 KB | Display | |
Data in XML | 1mc2_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1mc2_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/1mc2 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/1mc2 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14093.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: O57385 | ||
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#2: Chemical | #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: 1.45 Å3/Da / Density % sol: 15.3 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Details: Huang, Q.Q., (2000) Acta Crystallogr., D56, 907. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 1999 |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→10 Å / Num. all: 155596 / Num. obs: 73203 / % possible obs: 79.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.03 / Rsym value: 0.027 |
Reflection shell | Resolution: 0.8→0.83 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 0.332 / % possible all: 30 |
Reflection | *PLUS Highest resolution: 0.8 Å / Lowest resolution: 20 Å / Num. obs: 84242 / % possible obs: 76.6 % / Num. measured all: 384478 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 34.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 0.367 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 0.85→10 Å / Num. parameters: 11281 / Num. restraintsaints: 13526 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5.12% (include all data)
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 945 / Occupancy sum non hydrogen: 1210 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 0.8 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.1052 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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