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Yorodumi- PDB-1plu: PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1plu | ||||||
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Title | PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE | ||||||
Components | PROTEIN (PECTATE LYASE C) | ||||||
Keywords | LYASE / PECTATE CLEAVAGE / PECTINOLYTIC ACTIVITY / TRANS-ELIMINATION / PARALLEL BETA-HELIX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yoder, M.D. / Jurnak, F.A. | ||||||
Citation | Journal: Plant Physiol. / Year: 1995 Title: The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism). Authors: Yoder, M.D. / Jurnak, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1plu.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1plu.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1plu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/1plu ftp://data.pdbj.org/pub/pdb/validation_reports/pl/1plu | 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: 37733.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Cellular location: EXTRACELLULARGlossary of biology / Plasmid: HB101 / Strain: EC16 / References: UniProt: P11073, pectate lyase |
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#2: Chemical | ChemComp-LU / |
Sequence details | SEQ. IN SWISS-PROT IS PRECURSOR. C-TERM LYS WAS DISORDERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.84 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 Details: PROTEIN WAS CRYSTALLIZED FROM 1.0MM LUCL3, 1.0M AMMONIUM SULFATE, AND 50MM HEPES, PH 6.9 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jun 1, 1992 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHIC CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. obs: 24983 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUS PELC MODEL Resolution: 2.2→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / 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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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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