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Yorodumi- PDB-2ewe: Crystal structure of Pectate Lyase C R218K mutant in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ewe | |||||||||
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Title | Crystal structure of Pectate Lyase C R218K mutant in complex with pentagalacturonic acid | |||||||||
Components | Pectate lyase C | |||||||||
Keywords | LYASE / parallel beta helix / protein-oligosaccharide interactions | |||||||||
Function / homology | Function and homology information pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Erwinia chrysanthemi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | |||||||||
Authors | Scavetta, R.D. / Jurnak, F. | |||||||||
Citation | Journal: Plant Cell / Year: 1999 Title: Structure of a Plant Cell Wall Fragment Complexed to Pectate Lyase C Authors: Scavetta, R.D. / Herron, S.R. / Hotchkiss, A.T. / Kita, N. / Keen, N.T. / Benen, J.A. / Kester, H.C. / Visser, J. / Jurnak, F. | |||||||||
History |
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Remark 600 | HETEROGEN Only four of the five subunits of the pentagalacturonic acid were visible in the electron ...HETEROGEN Only four of the five subunits of the pentagalacturonic acid were visible in the electron density maps and could be modeled. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ewe.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ewe.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ewe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/2ewe ftp://data.pdbj.org/pub/pdb/validation_reports/ew/2ewe | HTTPS FTP |
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-Related structure data
Related structure data | 1airS S: Starting model for refinement |
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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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Details | The biological assembly is the monomer. |
-Components
#1: Protein | Mass: 37705.590 Da / Num. of mol.: 1 / Mutation: R218K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Strain: EC16 / Gene: pelC / Plasmid: pRSET5A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P11073, pectate lyase | ||
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#2: Polysaccharide | alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D- ...alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-CA / #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: 3.54 Å3/Da / Density % sol: 65.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: Grown in 1.0 M ammonium sulfate, 50 mM HEPES. VAPOR DIFFUSION, SITTING DROP, temperature 277K. Crystals then transferred to a solution at pH 9.5 containing cryogenic agents, 7 mM calcium and ...Details: Grown in 1.0 M ammonium sulfate, 50 mM HEPES. VAPOR DIFFUSION, SITTING DROP, temperature 277K. Crystals then transferred to a solution at pH 9.5 containing cryogenic agents, 7 mM calcium and 50mM penta-galacturonopyranose, and left to soak for 30 hours. |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→23.76 Å / Num. all: 28523 / Num. obs: 28523 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 22.9 Å2 / Rsym value: 0.031 / Net I/σ(I): 11.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pectate lyase C, PDB entry 1AIR, with arg 218 omitted Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 13.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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