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- PDB-1o8f: Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 30mM Ca2+ -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o8f | ||||||
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Title | Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 30mM Ca2+ | ||||||
![]() | PECTATE LYASE C | ||||||
![]() | HYDROLASE / PECTATE LYASE CLEAVAGE / CALCIUM BINDING / PARALLEL BETA-HELIX | ||||||
Function / homology | ![]() pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Herron, S.R. / Jurnak, F.A. | ||||||
![]() | ![]() Title: Characterization and Implications of Ca2+ Binding to Pectate Lyase C Authors: Herron, S.R. / Scavetta, R. / Garrett, M. / Legner, M. / Jurnak, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.8 KB | Display | ![]() |
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PDB format | ![]() | 60.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.2 KB | Display | ![]() |
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Full document | ![]() | 412.9 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o88C ![]() 1o8dC ![]() 1o8eC ![]() 1o8gC ![]() 1o8hC ![]() 1o8iC ![]() 1o8jC ![]() 1o8kC ![]() 1o8lC ![]() 1o8mC ![]() 1airS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37733.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 66.99 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.5 / Details: pH 9.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.9 / Method: vapor diffusion, sitting drop / Details: Yoder, M. D., (1990) J. Biol. Chem., 265, 11429. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. obs: 42615 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.18 % / Rmerge(I) obs: 0.0634 / Net I/σ(I): 7.79 |
Reflection | *PLUS Num. measured all: 178014 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AIR Resolution: 2.2→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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