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Yorodumi- PDB-1ee6: CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ee6 | ||||||
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Title | CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15. | ||||||
Components | PECTATE LYASE | ||||||
Keywords | LYASE / Parallel beta-helix / High-alkaline / Low-Molecular-Weight | ||||||
Function / homology | Function and homology information pectin biosynthetic process / polygalacturonase activity / pectate lyase / pectate lyase activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Akita, M. / Suzuki, A. / Kobayashi, T. / Ito, S. / Yamane, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: The first structure of pectate lyase belonging to polysaccharide lyase family 3. Authors: Akita, M. / Suzuki, A. / Kobayashi, T. / Ito, S. / Yamane, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ee6.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ee6.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ee6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1ee6 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1ee6 | HTTPS FTP |
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-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: 20947.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus sp. (bacteria) / Strain: KSM-P15 / References: UniProt: Q9RHW0, pectate lyase |
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#2: Chemical | ChemComp-CA / |
#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: 2.57 Å3/Da / Density % sol: 52.14 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: PEG 8000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 10063 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.204 / % possible all: 98.8 |
Reflection shell | *PLUS % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Resolution: 2.3→10 Å / σ(F): 3 / σ(I): 0 Details: Four disordered side-chain(1A,7E,20K,39K) were excluded in refinement stage.
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 10 Å / σ(F): 3 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.7 |